I had sent 4 diplomats to each of those factions earlier in the game and never refused a trade.  They actually were gifting me 175 credits through most of the game.  Was hard keeping factions liking me when there were wars, but judicious use of gifts and diplomats did the trick.

It's war.  It's their job to NOT have your interests at heart. 

Let me put it this way, there is no other game where a warring party surrenders to some randoms instead of the person they're at war with. It literally makes no sense to have an enemy besieged and on the back footing and suddenly he decides hey, let's give all my shit to some random faction.

I like the surrenders. A dying AI gets their last F U by joining someone they hate less. This will sound super nerdy, but remember when the Cardassians did that in DS9 and became a vassal of the Founders? Suck it Klingons! We surrendered to them, so now you don't win! Pretty much the same in Galciv, just with different race names.

Trade them to another civ for cash!