I win half of my matchmaking games against people that never choose starting territories or issue commands, then get booted after they hit the time limit. Can they be auto removed from the matchmaking queue?

If you mean real-time Quickmatch, then by definition: no. You have to click a button to join the queue, which acknowledges that you're there. There's no way Warlight can detect that you're not going to make picks and get booted.

No, I mean multi-day. I imagine that if you lose one game because you gave no commands, Warlight could see that and remove you from the multi-day queue going forward.

I don't think that exists, but once you get past a certain level you won't get this kind of opponent because they obviously don't have a lot of points.