This is actually quite common when playing AI. If you have destroyed their major fleets and have a significant empire/economic advantage, it will usually give you the win if there is no reasonable chance that the AI could field another major fleet and hurt you.

Well, as there is no leader, that condition can't happen, but wiping out all of their planets does give you a military victory, even if they still have a fully capable fleet that can beat you up and start new colonies elsewhere, many times they'll even give up before you've taken their last planet away from them.  Rebellion is said to have more win condition types, so we'll see what's been cooked up for us when that comes out.