OK, (I did a little research, to refresh my mind) it turns out the actual siege was by the FBI, so technically it wasn't a military operation, altho pretty much run like one.

I think my confusion lies in the fact that it seems to me that if this guy is not local, but we deliver a warrant, if he doesn't give up peacefully what is the recourse? I mean if we were to offer him a fair trial and he refuses, he has declared himself an enemy combatant right? (of course, it appears he has declared himself so any way, so it's a moot point) Enemy combatants can be taken out, problem solved. Or am I being too simplistic?

Think about it like this, even if the dude isn't shooting a gun, he is still a combatant, as generals rarely shoot guns, but in war one side does try to take out generals. Now while this isn't a war between countries, but more ideologies, and the combatants come from many different countries, including the U.S. it just seems to me that he doesn't rate a civil trial.