bs.
magnus would have dwelved as far as he wanted to whether or not emps taught him about bananas with condoms on.
magnus' attituide was one of comfort with the warp. his power and inexperience brought him down.
but since his legion was a bunch of freaks with more mutations than a chaos spawn before prospero whyd emps not end them
Initially the Emperor was just letting the Thousand Sons die off on their own because he couldn't fix them. Their name comes from the fact just under a thousand were left by the time they found Magnus, the rest had died to the Flesh Change by then. Magnus managed to fix it quickly by striking a bargain with Tzeentch, who was probably the originator of the Flesh Change himself. From that point on the 1k Sons were one of the most effective Legions despite being much smaller than all the others, so the Emperor had no reason (or time) to poke too deeply into them. He just hoped Magnus would heed his warnings thereafter and stop bargaining with daemons.
Especially considering the accusation Tzeentch throws at the Emperor to Magnus where he claims the Emperor made Magnus to be in the position the Emperor is in now when the time was right. According to Tzeentch Magnus' ultimate fate at the Emperor's hands would have been being bound upon the Golden Throne in perpetual agony as his psychic might was used to bolster the Astronomicon and the Webway. If that's true then Magnus was far too valuable for the Emperor to cast him aside prematurely.
It's also not like other mutant/deviant Legions weren't tolerated after all. The Space Wolves have a contagious degeneration into werewolves built into their genetic code, Sanguinus has wings, the Salamanders are all charcoal black with glowing red eyes, the Iron Hands practice self mutilation, the Night Lords are prone to prophetic visions and a cultural addiction to murder, the Word Bearer's are driven to find something to revere against the Emperor's express wishes, the White Scars are prone to being consumed by berzerker rages and losing control, the World Eater's kill entire planets for refusing to surrender, the Dark Angels compulsively keep dangerous secrets from everyone, Mortarion just flat out hated the Emperor, the Iron Warriors indulged in genocide out of frustration and what was essentially boredom,
If the Emperor had culled each Primarch or Legion that failed to meet the desired standard set in their design phase he would have been left with the Ultramarines, Luna Wolves, the Alpha Legion, the Imperial Fists, the Emperor's Children and the Ravenguard, and I'm not entirely sure about the Alpha Legion or Ravenguard.
You can't really discard 2/3rds of your greatest warriors and your own children because they have some qualities that make them evil in the small scale, and in the grand scheme of things even Angron and Kurze were essentially heroic figures, conquering entire worlds for the empire of Space Rome and killing entire species of creatures that ate children and breathed out poison, the loss of a few million or billion people per world to their faults would have been far outweighed by the people they saved in the long run had the Heresy not happened.