If the fighting has stopped, but the opponent continues to remain a threat, even in their compromised condition, you destroy the threat....plain and simple.
When it comes to you vs. them, you be the one sending the flowers!
Plain and simple.
Had Kirk rescued Nero and crew, they would still have been a threat, at least according to the movie. They would've tried to overwhelm the Enterprise crew upon beam over. The Enterprise would've been captured, and potentially used as a weapon against the Federation.
Now, in the novel, Ayel did make the point, once the Narada reached Earth, that they did not need to continue. The crew of the Narada were ready to go home. Nero rebuked him, and continued with his plans. So perhaps, by the novel, if the crew had overwhelmed Nero, and begged for rescue, Kirk could've done what he could to save them.
But, that wasn't the case in the movie. There was no indication that the crew would've mutinied to save their own skins. Nero spoke up as a continuing threat, and the crew would've been as well.
So, you put them down before they can ever threaten anyone else again.
Sorry, but that's how I see it. Someone attacks me in a fight, I do not consider them to be out to "kick my ***" as it were. I automatically consider them to be attempting to take my life, and in the process, I will fight for my life, not stopping until one of two things happen: They are incapable of fighting (for a prolonged period of time due to grievous injuries sustained by my efforts in preserving my life, possibly to the point of regretting they were ever born), or if they yield. If they yield, and then continue to act as a threat, then I will resume my alert status, and resume actively putting down the threat before they can ever threaten myself, or anyone else, ever again. You do not allow a potential continuing threat to get up and walk away. If you do, then the next time they come back, if they don't already immediately resume fighting (that would be a suicidal choice on their part), they may come back with "friends", or with a weapon.