I wouldn't say the Big E hated, im sure it wasn't war on a personal level, but as the man he was; the one chosen by the shamen of old Terra to unite and lead humanity against the evils of an uncaring unvierse he was bound to encounter some pit traps along the way. I always got the impression that the Emporer got on well with Eldrad on a personal level, alas thier differing view points put them at odds often. Nither come off as bloodthirsy, crude or prone to cruelty for crueltys sake.
Psykers are an odd one, but the judgements at the council of Nikea could well have been a safe gaurd against the machinations of the warp. Unchecked psykers make perfect pawns for the deamons of the immaterium, a risk not worth taking even with the ever growing philosiphy of the Imperial Truth so prevailent at the time.
We as people of the 21st Centurys are educated and conditioned, for the most, to be compasionate and caring for our fellow man, and accepting of other cultures. Unfortunatly the Galaxy of the 41st Millenium cannot be shared, and greed leads to war, even if its a war of our imaginations. As a human, and the Master of Mankind, the Emporer did what he had to do to bring humanitys destiny to fruition. His major floor was what made him so loved by his people; His humainty. He was a perfect example of this, warts and all, as the saying goes.