Sorry, what? Just because he doesn't mention Rayna in his few lines before falling asleep at his desk, he's really thinking primarily about Flint? He does mention Flint's loneliness and his own, neither of which would be so cast into the foreground if not for Rayna and her demise. He's feeling sorry for himself most of all - in particular, that his own loneliness led him to be taken in, caught off guard, risking his ship and crew as a result. He himself is the "flower dying in the desert," as Rayna says (repeating Flint's earlier description of loneliness). What he wants to forget is the Jim Kirk he'd become for those few hours on the planet. I don't think his feelings for Flint enter into it at all. Flint is no longer even human in some ways because of how his own history has changed him - outliving every woman he ever loved, for example.