Oh, haha -- yeah, the enemy ships will go nuts to try to kill it, and they get a bunch of progress if it dies. Your ships won't attack it unless you do the X-click thing once you control it, but still. Or if you nuked the planet, that would do it. The AI won't bother the settlements until you control them, but then all bets are off. Glad this was something simple, anyway.
The new release, D, is now out!