auto-recovering is a possible solution, but it's not really believable. especially in TFTD's two-stage terror missions, you probably wouldn't walk around and recover all items, because your main mission is to save the civilians - including those inside the ship. you don't have time to collect all the stuff. but if you are given the choice to take a turn or two more to pick up at least some stuff, it would actually make sense in in-game terms.
maybe the best option would actually be to force the use of the elevator? instead of advancing to the next stage once every alien is killed, the game simply informs you that all aliens in the current stage are dead, but you only advance to the next stage by bringing all your units into the elevator-zone.
on the other hand, this might cause some frustration if some random stunned alien recovers while you are moving to the elevator... the player thinks he's fine, but then the elevator doesn't work because there's another alien somewhere... of course, if the alien AI is reasonably aggressive (and actually capable of picking up weapons), this shouldn't be a problem. in the original, the frustrating "bug-hunt for the unarmed frightened alien" would be quite tedious.
