There is a way for Alderaan to make sense: It is unclear who captures/kills King Ulgo, but someone does. After that, there is a peace conference (Jedi Consular Class Quest). If the Light Side outcome is canon (which is most likely), all Houses agree to end the war. Alderaan stays neutral and the decision who inherits the throne is postponed.
The alternative dark side outcome is that all Houses (inlcuding Organa and Thul) agree that it's all House Ulgo's fault and they have to go into exile. Ulgo doesn't agree so they all form an alliance to drive them off the planet by force.
(I'm not sure how the Alderaan Bonus series interferes with this, though. I haven't played it yet.)
Well since both bonus quests involve the war going on, the Rep has them helping Organa fight Ulgo and to slow down their advance. The Imp has you fight Kiliiks while Thul beats up Organa.
So just ignore the JC world quest, cause the game sure does.