Ok I thought I would comment on this before I go to bed. I had to get up early this morning and probably should not be trying to answer such types of questions.
I have always understood that the body of Christ/the Church has been battled this whole time, so I don't know when you think it hasn't.
It goes on to talk about a city that He loves. I don't know any other city than that very special one....Jerusalem. Are you going to say that Jerusalem represents the church?