Yes, Onderon/Dxun plays in two parts. One that ends after you leave Onderon (when you've freed Dhagon Ghent and then met Kavar in the cantina) for the first time, and the next begins, or rather becomes available, the second you finish another planet.
So, as Cutmeister said, if you did part one of Onderon before doing Dantooine, then part two would become available. This is does NOT mess up your game - it just means that you can return to Onderon and finish the royal uprising on the planet. You don't have to, though - there is no time limit AFAIK, so if you want to do something else in the meantime, then Onderon (and Dxun) will wait.