Allies
Dealing with Khan was easy. He was one man with a small force and even smaller territory. Besides, Khan spoke openly without ploys or tricks. The Empire could seal and apply deals in hours with him, with no paperwork or time-consuming procedures.
Instead, the Global Army was massive and comprised countless individual parties. Dealing with it often involved days of research and even longer periods of negotiations. Each closed agreement usually stretched for years for those exact reasons, and changing its terms would always lead to heavy losses for one side.
Khan's presence on Baoway gave the Empire some leverage, and the planet's resources added another advantage to the equation. The Thilku could hope for something beneficial if they negotiated with the Global Army, but the matter wasn't without problems.