I have to agree with the OP. I loved the movie, there's almost nothing else I'd change about it. But that scene... I think it's very
Star Trek for Kirk to at least offer Nero the chance to surrender peacefully. It's something Prime Kirk would have done, and to me it's the moment when NuKirk shows how much he's matured since the beginning of the movie.
But Spock's petulant response, inner turmoil or no inner turmoil, rings untrue to me. It isn't so much that it's "making fun of Roddenberry's philosophy" as it is I'd imagine that Nimoy's Spock (you know, the guy who tried to broker peace with Klingons?) would have been in favor of the proposition. He may not have liked what Nero had done, but he'd put it aside. As Kirk said, that would
be the logical thing to do.
Of course, seeing as Nero immediately threw Kirk's offer back in his face, he was asking
for an ass-kicking.