On the subject of the patch alone, Shinobi, so what?By the Christian virus.
Now, I am a Christian, albeit a non practicing one, and I've never had anything against the fact that my Sensei is ALSO a minister who runs his own church (which most of the people at my dojo attend.) That was, however, until he made the announcement that we would now be assigned patches that had the kanji for "Army of the Cross" or an eagle with a cross infront of it.
Realistically, if he wants to use an 'Army of God' kanji as his school symbol, that is his right to do. If that is the school's symbol as of last month, then that is the school's symbol.
There are kanji and symbols in plenty of MA patches that have religious symbolism and the students of those schools are required to either wear the uniform or go elsewhere. They don't ask you to convert, but it is the symbol that the school owner or style has adopted.
Generally, a patch will be symbolic of the culture and philosophy of the style's founder. Like it or not, Christianity is a part of American culture. Nobody raises an eyebrow at Buddhist symbols or referrences in eastern martial arts because we just accept that it is part of the culture. Heck, if the teacher is a genuine Shaolin monk, that is generally looked upon as a plus!
So you have a school that was founded by a minister. While it may not be directly attached to his church, his philosopy will be infused in his teaching. That is his background and where he comes from. A school's philosophy will be to some extent an extension of the owner's.
Out of curiousity, what MA is he teaching? If you've stated this earlier in the thread, my apologies.
Daniel