Yeah I was thinking you could definitely give it some sort of bleed, but yeah if the mission ends before the device is out of juice you'll lose it, ideally you'll only want the device returned to the craft if it's intact as well as if it's snoozing.
I think I remember there were mods out there that allowed you to recover damaged armor, but I'm guessing they just used alien-corpses leaving us with a similar problem. Without being able to confiscate the inventory of the unit, or better yet the unit itself, there doesn't really seem a fix without making them disposable as stated.
Still useful, but not ideal for something like a portable turret, servo-skull, pokemon, RC car, etc, unless they're AI driven civilians i guess (which isn't awful).