"They'll never let you command a ship in this condition!" (In female body)
"She couldn't be happy being...only a woman."
There was also that one with Zefram Cochrane where they determined the entity was female by its 'feminine' behavior patterns, to which Cochrane was horrified. That was just plain stupid.
Also, TNG - The Host. DS9 made the Trill into an equal relationship between host and symbiant, but in The Host is was blatantly slavery.
In The Pale Moonlight is an interesting conversation. By Star Trek morality it's obviously wrong. But it also saved about a trillion lives and preserved the entire Federation way of life.
If you found out tomorrow that the Pearl Harbor attack was actually carried out by England in order to get the US into the war, how would you feel about that? (What if you were Jewish?)
Well the Host/DS9 Trill dependency is usually explained away by Riker not being Trill and therefore can't fully bond with the symbiont.
As for your Pearl Harbor scenario? As incredible a false flag operation as that would've been, my first response would be I'd want to go after the people who did that. That WW2 beat Nazi Germany, Fascist Italy and Imperial Japan is rather moot if it was British duplicity who killed over 2000 Americans and led the US to war. I'm sure if the Romulans ever found out the Federation assassinated Vreenak they'd go to war for sure. That makes them responsible, at least in part, for every Romulan who died in that war.
Is it a means justify the ends scenario? Sure... that doesn't mean there won't be hell to pay if it's ever uncovered.