Magnus had the loyalists hunting him, his choices where be hunted to death by the loyalists or stay out of the heresy, in which case the winner would come looking to kill him, or join Horus who although betrayed him would offer him protection.
Hunting him through the EoT? I can't imagine many Loyalists making their way to the Planet of the Sorcerers. The problem is though there is that Magnus chose certain damnation by joining Horus, while staying out of the Heresy and manipulating events to possibly save his Legion in the long run would be more logical.
Except their fall really isn't Horus' fault. No one told Magnus to use sorcery to try to warn the Emperor. In fact, the whole point of Nikaea was to get him to stop with the sorcery (well, not just him but he was still included). And the Sons still had the flesh change to contend with. Even without the Heresy something would have had to give at some point. The truth is the Sons were already fucked long before Horus turned traitor.
Indirectly it is. If Horus hadn't turned traitor, then the Sons wouldn't have been decimated by the Wolves for the reason they were. Regardless of whether the Sons would have been destroyed later by the flesh-change, or by breaking the Edict of Nikaea, I'm baffled by how quickly they accepted their lot. They may have been fucked before the Heresy, but Horus turning was the actual fucking, so to speak.
And why do they fight for chaos? Well, Magnus dedicated their service to Tzeentch. It was a price he paid to allow them to escape the wrath of the Wolves on Prospero. And what good would have come from sabotaging Horus? The loyalists weren't about to have anything to do with him and he already had a target on his back after the devastation he brought to Terra. Why piss off the traitors as well and be hated and targeted from all sides? Why hamper or destroy a potential ally for a cause he is no longer part of? He became a Daemon Prince, there really is no return to loyalty or redemption after that.
Running from possible destruction to certain servitude? Isn't much of a bargain there. I don't know I just see the Thousand Sons as smarter than that. They were the only Legion out of 18 that had the broadest understanding of the Immaterium, and they allow themselves to become slaves to a higher power? After centuries of teaching and training in the arts they roll over? Madness.
Why piss off the traitors and sabotage them? Well, the Galaxy was in the predicament it was in because of Horus' fall, and Magnus always held in his teachings that Humanity should be enlightened and cradled and guided and the like. I would have thought, that as a reluctant traitor Magnus would have held true to at least a smidgeon of these teachings? Why hamper a potential ally? Because that potential ally was the reason, directly or indirectly, leading to the Legions almost destruction.
And no return to loyalty or redemption, but vengeance against the main culprits perhaps.