I think I the answer is hidden in the Consular Storyline. At the end, there is a Peace summit. I would place the peace summit after King Ulgo is captured/killed. The outcome depends a little on alignment:
Before he officially betrays the Empire, Darth Malgus helps the Republic to undo almost all of the Empire's advances. The Empire can ship off some of the crystals, but Malgus grabs them. So Ilum goes back to Republic, basically the same as Corellia.