This suggestion struck me as easy to do and possibly efficient. So I did just that.
Oh my, I'm flattered

I could even make them some kind of security room, but not sure if it wouldn't make things too easy/dull.
Hard to say whether this will help or make the mission too easy without playing it a few times to check wether the military won't end up doing too well. Especially that the implemented solution can actually help you in a few ways already (military should be able to hold part of the base for a while, so you get less of "agents exiting the staircase and immediately being surrounded on all sides" (because the military should hold at least one side nearby) and you will most probably end up with one less corner to check for that last hiding enemy.
Speaking of searching for that one last enemy that - as people complained above - will probably be hiding somewhere deep in the base's vast ventilation network - is it possible to have this mission enable bug hunt mode, but maybe with a different message than usual? Something like "We managed to regain access to the base monitoring system" or something like that? It could trigger after XX turns or when there is only X enemies left.
EDIT: Just spitting out ideas here - I wonder if it would be possible to make the bug hunt mode turn itself on when the player moves an agent to a special tile located in a special room with a bunch of monitors or computers - what would simulate agents hacking into the base monitoring system - would be a cool feature or a side objective in this or other missions. Having a thing like that deep in human-made bases would immersively ease the hassle of finding the last few enemies once you practically already won the battle anyway. And in alien bases too, but only after you researched their technology enough to be able to hack into their systems.