Yes, Magnus the Red is short-sighted and arrogant as all get out, but at least part of his motivation for going way off the deep end had to be the fact that the flesh change was a deceptively simple issue to solve.
Imagine: You're the pinnacle of your species, elevated above all others, able to comprehend and apply forces that could tear another's soul apart. Your warriors spontaneously exploding into writhing goo sounds catastrophic on paper, but at the end of the day, it's just a metaphysical medical issue. Not terrible, considering what other legions have to deal with, right?
And yet, no matter what you try to fix it, nothing works. The problem persists and you start getting desperate, frustrated. You're supposed to have all the answers! You're the scholar, the mage, the keeper of the arcane. Peering under the veil of reality to commune with its tumultuous undercurrent is just Tuesday for you. How does such a simple little puzzle like this continue to stump you?
From what I've read, Magnus seems to work best whenever he's paired with someone more grounded. Not just to keep him from skipping off down a new research rabbit hole every two minutes, but to support and stabilize in general.
Being a psyker in the Imperium is already a very isolating position: you're constantly regarded with suspicion, your primary worth lies in how your unique properties can be harnessed for the benefit of others. Magnus thinks he can't rely on anyone else to help him, both because he thinks no one else could understand and of the risk of attracting the wrong kind of attention and getting his legion censured permanently.
In comparison to other traitor primarchs, Magnus sticks out to me because his primary goal isn't even directly related to the rebellion itself. He just keeps desperately bashing his head into the same brick wall of a problem repeatedly, ignorant to the fact that that method is exactly what caused his legion's situation to spiral in the first place.