User blog comment:Primarch11/Guilliman Heresy/@comment-3245042-20120615152958/@comment-2253300-20120615155200

There is basically three issues with the Thousand Sons.

1. The Flesh Change. The uncontrollable mutation of the Thounad Sons' Gene-seed. It is a genetic flaw that poses more danger than the Blood Angels' Black Rage and Red Thirst. Even the Emperor, who created the Space Marines and was probably the most scientifically knowledgeable human of the time could not fix them. This mutation would have lead the Thousand sons to either destruction or desperation.

2. Sorcery. According to what I have read the Flesh Change was supressed when Magnus unwittingly struck a contract with Tzeentch. Not to mention that the people of Prospero and the Thousand Sons practiced this forbidden art often. Basically Magnus was under the influence of Tzeentch without knowing it. Tzeentch had his claws buried deep in this Legion from the get go.

3. Psykers. The Thousand Sons have an overwhelmingly huge proportion of Psykers in their Legion. With so many Psykers the potential for Chaos corruption and Daemonic possession within this Legion are huge. Now alot of people like to point to the Blood Ravens as an example of a loyal Chapter with many Psykers, but this is different. The Thousand Sons used Psychic power as a prerequisite for advancment in rank. Nearly every sergeant or above was a Psyker, and this meant that the leadership was at particualr risk for corruption. Even if you could work around the first two issues this one would nail you.

So basically I agree with you that Magnus was in his heart a loyalist, but i think the circumstance of his Legion would have pushed the Thousand Sons into heresy, Burning of Prospero or not.