Argus Van Het said:
I know I'm just enjoying how to torture this poor player, but I've always be a devious GM, with the motto "reap what you sow"
Forgive me for saying so, but it seems to me your motto is more like "punish them for succeeding"
I understand you want the capture of Eldar to be a significant event, but murdering the players whatever they do is merely going to make for players who don't take chances and feel they can't succeed. That kind of thinking may have some place in the Grimdark future, for some characters, but you don't want players feeling that way and Rogue Traders are hardly your run of the mill "never get ahead" types.
(that said, yeah look out for diseases - cross race breeding is full of dangers)
As for showing them mercy, I'd call that an awful idea ... you might spare yourself a smidge of Eldar wrath, but you still destroyed four of their ships and - what, hundreds? - of their people ... they aren't likely to look at the gesture and think "how marvelous, let's be friends!".
I didn't read all of this forum. Only wanted to say that some GMs need to learn when to say "No."