I don't think he predicted all out war with Chaos. My thoughts are that he was trying through suppression of religion and psykers to weaken the chaos gods. And to assuage the fears of a lot of Imperials about psykers and their power. I mean look at the council of Nikea and a lot of the primarchs even were afraid/concerned by psychic powers, hence why the edict went through. If he bans it then a slight majority of legions and primarchs will have their fears assuaged and the amount of energy the Chaos gods have to mess with is reduced in one fell swoop.
However I agree that it is shown that he would have had an easier time had librarians been more prevalent to see the betrayal coming, deal with Daemons and counter traitor librarians. But hindsight is 20/20.