A guy I work with raises a similar question about the ending of Star Trek (2009):
At the end, Kirk offers assistance to Nero as his ship is being pulled into the black hole. Spock initiates a quick sidebar and disagrees with this decision to extend help (understandable, since Nero destroyed Vulcan). The discussion is rendered moot when Nero says he would rather die, blah, blah, blah.
The guy claims that this is ending goes against the Trek tradition of not killing and trying to save lives, even when it's the bad guy. He may have a point - it does seem rather un-Trek like to kill off an enemy.
For example, even during multiple encounters with Khan, Khan was never killed off (in Wrath of Khan, it was Khan who destroyed his own ship as a result of deploying the Genesis device), despite being probably the most notorious villain in the Trek universe.
Personally, I wasn't all that troubled by this scene, though I would tend to agree that it was a bit un-Trekish.