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Uh, everyone is a pawn of Tzeentch.

Okay, all joking aside. The First Heretic suggests that the Emperor did indeed have the help of the Ruinous Powers to create the Primarchs. However, rather than serving the Gods, he intended to double-cross them by hiding the Primarchs behind a Gellar Field (the same anti-Warp shield that starships use) so that the Gods could not influence them. This plan only fails because the field goes down (thanks to time travel shenanigans) and the Primarchs are abducted.

In short, using the Primarchs as a force for disorder and Chaos may have been Tzeentch's plan all along, but it certainly wasn't the Emperor's goal. He simply thought of himself as a better schemer than Tzeentch... Which, I guess paradoxically makes him a disciple of the Changer.