We honestly have no idea whatever happened to the Organians. Certainly, we never see them intervene in corporeal affairs again, in any of the post-TOS movies or TV series.
My pet theory? At first, in the years after "Errand of Mercy," neither the Federation or the Klingons really knew how hands-on the Organians were going to be when it came to enforcing the truce, so the possibility of the Organians intervening acted as a deterrent, but as years went by and the Organians kept to themselves, on a higher plane of existence,the Klingons started pushing the envelope . . . while carefully steering clear of Organia, of course.
Which brings us to their aggressive behavior in their Kobyashi Maru simulation. (And the fact that that was just a hypothetical training exercise also provides a bit of wiggle room.)