It most certainly does. The only problem you have with your statement is that church is not found in scripture and even the translations that include church do not capitalize the word.
Matthew 18:17 And if he shall neglect to hear them, tell it unto the church [ekklēsia]: but if he neglect to hear the church, let him be unto you as a heathen man and a tax collector.
The word there is ekklēsia which means an assembly or congregation. The RCC or any organization like it is NOT what is referred to there.
>>It does not seem very prudent to refer to that Church which Christ loved so much as "the whore of Babylon".<<
I have not fallen under the cultic oppression and lies of the RCC to believe that it is the body of Christ. With its inclusion of paganism it cannot possibly be the body of Christ and is most likely the whore of Babylon as described in Revelation.
Oh heck - let's read the bible written in ALL caps!!
http://en.wikipedia.org/wiki/List_of_New_Testament_uncials