************This is a spoiler from Angel Exterminatus********************************
I don't think that the Emperor caused the rebellion, although there are certainly hints to it. One of the very good things about they HH books is that things are told from different perspectives. Anyway, why i don't believe he is responsible is because:
In a flashback of Perturabo talking to the Emperor, the emperor mentions that he can no longer see the future.
It also heavily implies that his entire purpose for creating the primearchs and spacemarine legions was to defeat Chaos.