heck, consider the most famous case of soldiers using a church as a base of operations for military action: The Alamo.

now, mind you, Santa Ana at least spared the civilian women and children and all that, but it was still techincally a church mission being used as a military base.

Of course, maybe that makes us today worse than Santa Ana then, because he spared the non-combatants and we just bombed the heck out of this thing outright. maybe.