In his article The Translation Conspiracy David Hargis writes:

"The word church is not in the original Bible. The word

church comes from the old English and Germanic word
kirke, (pronounced "keer - kay"), and which itself came
from the Babylonian for the goddess Circe (pronounced
"seer-say"). This is the word from which we get circle,
circumference, circumstance, circumvent, etc. The
goddess Circe was thought to be connected with the
power of the sun, which is round, and thus the connection
to Circe, a circle. In anglo-saxon history, the pagans
worshipped the sun standing in a kirke, a circle. These
pagan worshippers became known as the circle, or the
kirke, then ultimately the church. Yes, pagans were called
the church before Christians were called the church.
Therefore, church means, at the least, a pagan circle for
worship, and at the worst, the worship of the goddess
Circe, or the worship of the sun."
I'd like to briefly address these claims: The word church is modern English, and
naturally is not in the original language of the New Testament (Greek), but this
is irrelevant. The etymology of church that he propagates is simply not true and
his statement is full of historical and morphological errors. For one thing, kirke
was not Old English but Middle English, and a West German form at that.
Furthermore, it does not derive from Babylonian, but from the Old Saxon form
kirika or kerika. This word was the Germanic form of the Greek term kuriaka or
kuriakon and means belonging to the Lord. The Goths were using the term
before Christianity reached them, but it was not because the term was one of
their deities. There were Germanic mercenaries who worked for the Roman
Empire before its fall in the 5
th
century as well as Gothic raiders in subsequent
days, and these people would attack churches and pillage them, stealing sacred
vessels and various objects. They learned this word because the sacred
objects and the buildings themselves were called kuriaka (belong to the Lord
or of the Lordin this article I use the plural rather than the root form
kuriakon/kuriakos). The use of this term goes as far back as the 3
rd
century.
The word Circe he refers to is not Babylonian but Greek, and its modern
pronunciation varies. This Greek name is written as Kikq (Kirke) and usually
pronounced as keer-kay. The connection with the Babylonian Ishtar is
debated among scholars and is not so obvious as Hargis claims. But the
Babylonian relationship is still irrelevant because theres no proof that the Goths
worshipped Circe anyway. At best they seemed to borrow Greek terms. The
burden of proof rests on Hargis and his camp to prove that the term church in its
Old English form really was used of pagan centers of worship.
On the contrary, there is vast literary evidence (as the OED illustrates) that the
Greek term kuriaka was used of sacred objects and church buildings since the
3
rd
century and that the Germanic peoples adopted the term into their
vocabulary as kirika prior to even the 5
th
century. This influenced the Old
English spellings as cirice, cyrice, and circe (remember that the c is hard like
k). The spelling of circe being same as the Greek mythology figure is
coincidental, for although they appear the same in Old English they do not
match at all in Greek (kikq vs. kuioko). The figure below shows the
evolution of the word church from its original Greek form kyriaka (kuioko).
Remember that the English c in the 11
th
and early 12
th
century are pronounced
like a k.

YEAR VARIOUS FORMS OF THE WORD "CHURCH"
1600 church becomes common spelling during long process of standardization.
1500 church, churche, chirch, chirche, chyrch, chyrche, church, cherche
1400 churche, chirch, chirche, chyrch, chyrche, cherch, cherche
1300 churche, chirch, chirche, chyrch, chyrche, cherch, cherche
1200 churche, chureche, churiche, cherche, chereche, chyrche, chyreche, chireche,
chiriche, chirche
1100 chirche, chiriche, chireche, chyreche, chyrce (Middle English period 1100-
1500)
1000 cirice, cyrice, circe, cyrce (Old English/Anglo-Saxon period 600-1100)
300+ kirika, kerika (W. German/Old SaxonPre-English period)
200+ kyriaka/kuriaka (Greek)

In fairness, there are some dictionaries and some scholars who disagree with
this standard position. This should not be surprising though, since every field
of study has its fringe movements with adherents who reject the established
party line. For example, Ebenezer Brewer in his Dictionary of Phrase and Fable
under the entry church rejects the Greek origin of the word:
this is most improbable, as the word existed in all the
Celtic dialects long before the introduction of Greek. No
doubt the word means a circle. The places of worship
among the German and Celtic nations were always
circular (Welsh, cyrch; French, cirque; Scotch, kirk;
Greek, kirkos, etc.). Compare Anglo-Saxon circe, a
church, with circol, a circle.
By arguing against the Greek influence on the term, Brewer discounts the
possibility that the Circe of Greek mythology is even an equation in this issue.
The real issue, he believes, is that church developed from the word which we
now call circle, which was the method of assembly for these pagan rites. One
problem with this is that churches were not circular, but rectangular. Why would
pagans call a building circle when it clearly wasnt. This is like the proverbial
square peg/round hole saying. The fact that the words have similar or
sometimes identical roots does not mean that the meaning of one should be
read into the meaning of the other. In his book Exegetical Fallacies D.A.
Carson calls this a root fallacy:
The search for hidden meanings bound up with etymologies becomes even more
ludicrous when two words with entirely different meanings share the same etymology.
In his book, Carson then compares two Hebrew words with quite different
meanings. Lechem (bread) and Milchamah (war) both have the same
etymological root lacham . Conjectures may abound on why the words are
related, but it is irrelevent. Language evolves, and part of that process is the
change of a word's meaning. For example, the English word "nice" comes from
the Latin nescius, which means arrogant and "gentleman", which used to refer
to a man from a certain social class regardless of manners, now refers to a man
who behaves honorably toward women (though even now the term is changing
to mean something less). Words cannot be defined strictly by etymology, but by
usage. When the Israelites called their deity El they were not worshipping the
Canaanite god from whom they borrowed the term. When Arab Christians refer
to God as Allah, they are not worshipping the Muslim god of Muhammad, nor
are they worshipping the moon god from whom Muhammad took the term. So
even if it could be proven that the word church really came from a pagan term,
what would that mean? Can language not be redeemed and used for Gods
glory?
There is also a logical fallacy here. If its improper to call the building a church
because that word once had a pagan connotation, then it should follow suite
that it is wrong for Christians to hold hands in a circle for prayer or draw circles
or live in a round house, etc. since circles honor the Sun and reflect the
customs of pagans. The days of the week would need to be renamed, since
Sunday is the day of the Sun god, Monday honors the Moon god, Thursday
honors the god Thor, and Saturday is Saturns day. Believers would have to
select carefully what car they drive, since many names are derived from Greek
mythology. This list would be endless. Does this sound ridiculous? Yet this is
the natural conclusion to this worldview. Once again, Hargis:
(Exo 23:13 KJV) "And in all things that I have said unto
you be circumspect: and make no mention of the name of
other gods, neither let it be heard out of thy mouth." We
are commanded not to even mention the names of other
gods! What does that portend for the ubiquitous use of the
word church, which is the name of a pagan god? And to
add insult to injury, notice how the King James says, "be
circumspect" which is a form of the root Circe! Actually
the word in Hebrew is shamar, which means to guard
against. The L-RD has commanded us to guard against
the mention of any other god, not to make a circle against
it. See how far we have been from the truth! G-d help us.
Hargis errs again by reading into circumspect what he believes is the root
meaning of the word. Websters 21
st
Century Dictionary lists the meaning of
circumspect as cautious, which is consistent with the Jewish Publication
Society's translation of the above passage as "be on guard." The translators of
the King James Bible understood this, which is why they chose this word. They
knew that circumspect comes from the Latin circumspectus, the past participle
of circumspicere, which means to look around. The word then carries the
meaning of being on the lookout or on guard, which is consistent with the
Hebrew meaning. Yet once again, Hargis didn't research his claim before
publishing it and has villified a classic translation unjustly. It is evident where
this doctrine leads-- that God does not want His people to even use terms like
circumspect, circle, circumference, circumstance, circumvent, etc. It is
unimaginable how far this can go. Yet it could all be avoided by more carefully
researching the issue.
The case for church meaning belonging to the Lord is a strong one,
recognized and defended for over 1200 years. Though there are variant
opinions, they have not swayed the majority. Until the issue is more settled
among English scholars and linguists, it is highly improper to be dogmatic in
favor of divergent views. In their polemics, Hargis and others have condemned
many without warrant. This unfortunate, baseless rhetoric only further divides
the Body of Christ and gives the Messianic movement a bad name.
Although this article has dealt with the etymology of the English word church, it
has not addressed the issue of how to translate the Greek word ekklesia,
normally translated as church, nor has it dealt with the distinction between
ekklesia and kyriaka. The purpose here has been to show that the English
word church does not have a pagan origin, but a sacred one. It should be noted
that the Biblical term ekklesia refers to Gods people as a community or
assembly, whereas the later term kyriaka refers to objects or buildings set aside
for the ekklesia to use. It was a post-Biblical practice to use the terms
synonymously. Nevertheless, modern usage follows this practice so that today
the word church may be used to designate either a building or an assembly.
Sources:
The American Heritage

Dictionary of the English Language

"CHURCH": From God or From Man, by Dusty Owens
Church or Ekklesia,
http://members.tripod.com/jbrooks2/CHURCH_OR_EKKLESIA.html
Circe (Church)--Daughter of the Sun by Gary Amirault
Dictionary of Phrase and Fable, by Ebenezer Brewer
Encyclopedia Britannica, 1911 ed.
Exegetical Fallacies, by D.A. Carson
Merriam-Webster Online Dictionary
The Oxford English Dictionary
The Translation Conspiracy, by David M. Hargis*
Websters Dictionary, 1828
Websters 21
st
Century Dictionary
The World Book Encyclopedia
*David Hargis has since passed away since the writing of this article