I'm sorry, but you are basically trying to compare the War of 1812 to Iraq and Afghanistan.
Not. The. Same.
Separation of church and state? Probably not guided by what's on our money....however, if I was against believing in a divine power and the pledge my kids said at school had "under God" in it I might be annoyed at best. It's really a bit outdated, and by no means universal.
All in all, this stuff is tiny potatoes considering we have a useless Congress and weak President who can't even find a way to get them to compromise and move on from what is supposed to be day to day business. Our government is becoming even more inefficient and expensive. A much bigger concern than the national anthem.