Hm. Well, if it's deliberate that it steals stuff from the abandoned base... I disagree, but I can just mod in an exception. (Or, I suppose, invest in leadership and cart around a fleet of cargo vessels. But that's a bit silly.)
On stealing ships: Maybe put this in supply fleet generation? Should be possible to see if you're likely to hit the cap, and then if necessary remove random ship(s) of the same size as what you're bringing. (Not perfect, since player or even another supply fleet could add or remove ships before the supply fleet arrives, but eh. Should be close enough.)
Or, simpler: only steal a ship if there are at least two of that hull present.
Also, the game does wonky things if you reduce a crew stack to zero. Should maybe try to avoid that? (Sadly, I haven't poked at the details enough to know exactly how this can happen, just that it did.)
Might also be worth making SupplyControl reduce crew (and marines!) by a percentage of how far they are over some limit; marines in particular can, at the moment, only be removed in chunks of (at most) 36, which has resulted in the RSF station in my current game having a stock of 10,000 marines...
Um. I guess I should probably also make it clear that I think this is an awesome mod; I wouldn't be playing it enough to give this kind of feedback otherwise. I especially like the XLE faction's ships. ...Which, given my chosen forum name, should probably come as no surprise.