[...] For goodness sakes, the production workshops shouldn't even have doors to the outside world. [...]
As far as I remember, they didn't have doors in the past, but then, as smoking was prohibited inside, the trade union demanded that they added the doors for the workers.
Adding some weird looking civilians with move 0 as some breakable things in command center and antimatter storage has been suggested before, but perhaps the devs have a better plan and try to avoid such temporary hacks.
About pathfinding, that sounds like it might be a non-trivial problem. I am wondering how difficult would it be to make aliens not know the location of humans unless they see them, or at least not try to move towards humans (but move randomly) unless they can reach them in a few turns? I have read some alien aggressiveness setting being mentioned in the forum, but no idea where it could be found to try lower aggressiveness which might alleviate the problem of getting stuck.