As far as I know rescuing them wasn't the problem. I mean Spock, who really didn't want to break the prime directive, was totally fine with it, too. He went into the volcano with that cold bomb after all. The problem was only, that they were seen by the indigenous species. They even started unintentionally a new religion. If Kirk would have let Spock die and the Enterprise wouldn't have been seen, Kirk wouldn't have gotten demoted.
Either way I guess the long term future of the Nibirus might be something like in this short fanfic:
https://www.fanfiction.net/s/10591101/1/The-Planet-Nibiru
If they somehow remember the stories of their forefathers at all, most of the Nibirus likely won't truly believe them and think they are only old sagas, which aren't based on reality. And when they reached the point, that they know for sure, that alien life exists and maybe even meet humans, they are advanced enough to handle that knowledge.