You know what, I think it would be impossible to to a Star Trek without a message. It's so much a part of it, even if it is implicit, like ST11. It's woven into the characters.
I don't know. A lot of Star Trek stories I know that have the crew deal with evil characters usually ends with the our characters not killing the bad guys in some way, shape or form.
- Kirk doesn't kill the Gorn commander in "The Arena".
- Kirk doesn't kill Kang or his crew "Day of the Dove".
- Kirk doesn't kill the Romulan commander in "Balance of Terror".
- Kirk doesn't kill Khan in "Space Seed".
- Kirk doesn't even try to kill Balok in "The Corbomite Maneuver".
- Kirk decides not to kill Karidian in "The Conscience of the King".
- Despite being an entirely evil version of the crew, Kirk doesn't want to kill anyone in the Mirror Universe in "Mirror, Mirror".
- Even though they were fake and there was the possibility for success, Kirk and crew didn't kill the Earps in "Spectre of the Gun".
- Kirk refuses to destroy the Klingon attack cruiser in "Elaan of Troyius".
- Spock and crew don't destroy the Tholians in their retaliation efforts in "The Tholian Web"
- Kirk doesn't kill Garth in "Whom Gods Destroy".
- Kirk doesn't kill Kruge in Star Trek III until he is absolutely forced to.
Now, I'm not saying Kirk is a total pacifist, but these are the details. There is no reason I can think of why Kirk couldn't have beamed over the Romulan crew onto the Enterprise like he did in "Day of the Dove".
But it was all for nothing. I actually thought that Kirk's idea of making peace with Romulas was the only selfless thing he did in the whole movie, yet Spock's development went from a character who would normally show compassion to someone who would rather see the enemy dead than making peace with an entire civilization.