One of the most popular criticisms of A Thousand Sons, and the elaboration to date of the HH, has been that the trial at Nikea was retconned in a way that is inconsistent with what we "know" and that is illogical. Here we can see the basis under which Guilliman is going to effectively reverse parts of the edicts of Nikea when he formalizes the Codex Astartes - it seems likely he'll champion the revision of the ruling to be sorcery is banned, psychic powers under the guise of Librarians are ok.
I think the last few books of the series, in particular Know No Fear, but also the Garro series, have given us sufficient elaboration of the implications of Nikea to say that the new version of the Edict of Nikea isn't a stuffed up retcon or mistake - the retcon is a deliberate addition of a new strand to the Heresy story - one that potentially will add quite a bit to the overall story arc.
Know No Fear showed Guilliman crystalizing what lots of the complaints about the total ban on Astartes practising as psykers had been getting at.
So the situation we saw as at the end of the A Thousand Sons/Prospero Burns duology wasn't the full picture, and isn't how the situation will stay, even during the Heresy itself. It seems to support what was suggested in Prospero Burns - that Chaos had its claws all over the trial at Nikea and its outcome - for reasons beyond just ensuring Magnus fell.
Doesn't explain why the Emperor fell for such manipulation, but besides the suggestion in Outcast Dead , the questions about why the Emperor wasn't more astute in preventing the Heresy are always really hard to answer, but are necessary parts of the entire story.
I belive the reason the Emperor did as he did at Nikea, was to stall the coming civil war. He knew the consequences of the edict, and what forces that worked behind the curtain. Yet I belive the way he did things, resulted in the outcome that would prevent the heresy the longest amount of time.
Had he just slapped Leman Russ and Mortarion, and told them to get over it, the tensions could easily have started the war much earlier.
And to try and explain why The Emperor didn't prevented the heresy (tough he tried all he could) i'm going to quote myself from a previous thread about the Outcast Dead:
"He is a person who has one goal above all else. The peace and continued survival for the human race. Sacrafices must be made, and the hardest choices immaginable must be chosen. As humans are now, the way we are going to go out in the universe, will either be by natural disaster or war (either between humans and humans or against xeno). Either way our doom will be violent and painful. The Emperor is the only human, able to lead humans along a narrow path that leads to an end, not clouded in war or disaster.
As he himself says, it's not possible to be all powerful and all knowing at the same time. To lead the human race to "victory", he has to sacrifice his ability to shield them from themselves (in the form of Horus and his legions). And that's probably why the Heresy was allowed to happen.
I've seen people talk about how a genius like The Emperor, capable og seeing so far into the future, can not see the Heresy coming and prevent it. The answer is he has, but he simply dosen't have the power to prevent it. He can only try his hardest to win or make it a draw. "