Both of the dojo I train at stopped putting anything kind of shrine or kamidana in the kamiza area just to eliminate any potential issues. One has an American flag, the other has a chalk board.
Personally I'd find it far far more creepy to bow to a political symbol than to a photo (especially in the context of a martial art where we are constantly bowing to other humans in a mutually respectful but totally non-worshiping way). I would not be comfortable bowing to a flag at all. YMMV.