>>23391065
It isn't a traditionally structured war but Yuuki Yuuna has a huge amount of the drama be very "military-esque" how the girls know that it's their duty to fight but they might not be happy about it. KuMeYu is practically a war drama in itself, just that it focuses on a group of scouts that don't directly engage with the monsters.

Also there's stuff like the Kamen Rider OOO novel where Eiji fights terrorists. Not mahou shoujo but a lot of mahou shoujo in a war environment would probably be like that since they are typically not tied to a chain of command.