As outlined at the Council of Nikaea, psykers were not banned outright but instead severely limited. Their potential as a weapon on the myriad worlds of the Imperium of Man is not only obvious, but necessary for the continued struggle against the Chaos and the multitude of heretical, alien, and destructive forces which seek to undo the great works of the Emperor.

Still, I believe you refer, instead, tot he fact that psykers are not allowed to wander fee and unfettered in worlds populated by Man; for this instance, we need only delve into the nature and source of the Psykers' powers; the immaterium. Given that the immaterium is peopled - or rather haunted - by demons and destructive forces of Chaos, and similarly given that psykers must tap into the immaterium, it was concluded that psykers were a danger due to the very real possibility that they might be possessed by demons and wreak havok upon the worlds of Man. Human brains - and their latent psykic powers - are not as refined or evolved as, say, the Eldars', ad as such offer an opportunity for the Chaos to spill forth onto worlds. Imagine the destruction psykers could wreak in a densely-packed hive world, for instance as happened in the Age of Strife.

Still, psykers serve an important function within the Empire; they feed the unlife of the Eternal Emperor of Man as well as power the beacon - the Astronomicon - which allows successful navigation through the Warp. It is understandable, though, that some mutant psykers are killed on some (if not many) planets despite their value tot he Empire. A tragic fate, indeed, but less so than the danger they present if left unchecked on distant worlds.

I hope that answers your question, I am certain that my colleagues here will point out any shortcomings in my recitation of the reasons behind the decision at the Council of Nikaea.

Sources:

The Inquisition by Gideon Ravenor

The Blessed Decree of the Council of Nikaea: Psykers and their origins by Gregor Eisenhorn