Seriously for just a moment, I think Kirk would likely offer him the chance to stay on the ship but leave it to Cupcake to choose if he felt he could serve under Kirk's command. If he was able to I could see them becoming friends. (Assuming Cupcake didn't get killed by a poisonous flower or beamed down to a planet that wasn't there or.... Well you get the picture.) If not, then I could see Kirk writing a solid recommendation for a man with enough integrity to admit there was a problem with him staying on the same ship.
Ever notice that many of the same people who want variety in life frown very hard on vanilla... But without Vanilla, Baskin Robbins just wouldn't BE 31 flavors.