Board Thread:Warhammer 40k General Discussion/@comment-25618639-20141206200938/@comment-25177957-20141217104758

Some sort of madness was bound to happen regardless of if the Great Crusade was completed, the Primarchs couldn't simply be kept in apartments, so they'd ether war against eachother, try to leave the galaxy to conquer more, or simply become madmen after hundreds of years of being caged in an apartment. The Emperor would probably have to just allow them to govern their own portions of the galaxy if he wished to keep the peace. But since the Primarchs were made for war, and wanted to wage war more than anything, they'd find war, and some would eventually fall to Chaos anyway.

And no...The Emperor would certainly not "dispose" of them, the Thunder Warriors were cruel tools and were engineered to conquer galaxy, only to conquer Terra, If the Emperor tried to simply kill of the Primarchs, the Emperor would be destroyed before he could begin such a plan. Plus of all, the Primarchs were the Emperor's most precious creations, look at how reluctant he was to destroy Horus at the climax of the Battle of Terra, even if Horus was trying to kill the Emperor. Based on that model, I'm not sure why anyone would think the Emperor would just get rid of them.