I think the morale penalty for being at war with a species should wear off 50 to 100 turns after you finish conquering them. I defeated a civ about 200 turns ago and their citizens are still mad.
Actually, this gives me an idea, wouldn't it be neat if different species kept their conquered moral penalty for different lengths of time?
My head cannon for them never forgetting has been that I keep bringing it up. every time I call up their old homeworld I awkwardly blurt out:
"hey remember that time when I lit your cities on fire? with lasers? from space!?! heh, wars am I right? oh hey, you still have that statue by the capital-?"
*furiously whispering advisor*
"oh.. we- oh dear, for a manufacturing district? ouch. mhm. yeah sorry about that, but hey, you wanna make an omelet you gotta break some eggs! which reminds me, I just dropped by to strip mine your planet so..."
*click, click, scribbles signature on data pad*
"Perfect, I'm gonna head out, you guys have a good one!"