For ST09, I'm left wondering what purpose the scene with the discussion of what to do with Nero serves. Is it to show that new Spock has a bloodlust? Is it to show that Kirk is willing to entertain alternatives? Is it to show that Nero is an asshole? Is it to show that they even have time to entertain such decisions? I think it's primarily to make the audience feel good by toppling the bad guy they so easily built up. Everyone loves to see the bully get his comeuppance in a movie, and this is just playing to that trope.
I just think that the way they handled the scene didn't work out. Kirk was realistically going to offer assistance when they could barely escape themselves? Why even offer such a thing if it's truly just a battle situation? That the alternative is even raised is why this is an issue. It implies there is actually time or ability to do something. If it had cut from the Jellyfish colliding to the Enterprise opening fire, I don't think I would have a had a problem with it.
Yeah I think this probably sums it up. It was the tone of the scene that was wrong for me. But it is a trope that crops up in many movies because movie-goers love to see villains get their cumuppance. It should come as no surprise that many people have no problem with the scene - they are the audience for whom it was intended.