Lucasarts was distributing a new pressing of KOTOR 2 not that long ago. You may even find it on shelves right now, in fact. So them having something against the game doesn't strike me as true.
There may be some technical issues relating to it. Valve does turn down games, even from known publishers and franchises, on technical grounds. Just try to find the second Splinter Cell game. But 1, 3, 4, and 5 are all there.