Magnus shed what remaind of his loyalty to the imperium of man and to the Emperor when he refused to be killed by Russ, up till then all his actions were still
[TSons Fanboy Mode]
Woah, now. Magnus was probably the most loyal Primarch, with the most loyal Legion. He was utterly loyal to the Emperor; so much so that he even denied a direct order from the Emperor in order to try and warn him about the betrayal. He could have obeyed the Emperor and not used his powers, and then the Big E may not have been warned about Horus. But so devoted was Magnus to the Emperor that he was prepared to earn his wrath to help and serve him. If that's not loyal I don't know what is.
As for refusing to be killed by Russ... come on, man! Russ starts landing troops everywhere and killing Magnus' Legion and *still* Magnus doesn't get involved. He waits until they've pretty much been screwed over before thundering down and turning on god-mode. If Russ had just made a strike at Magnus, rather than the whole bloody planet first, he may actually have come quietly. Instead, the dirty great Space Wolf decided to raze Prospero and its Legion first to get Magnus upset. He's got the subtlety of a nuclear missile, that one.
I've yet to read Prospero Burns, but I'll have to keep a Thousand Sons nearby in case I ever need to brace myself for the heretical anti-TSons propaganda I'm likely to read within.