Supposedly Raz is the 'champion of free will', and a proud one at that; I'd say it was never going to go smooth if he was, and there was this thing being worshipped as a god, forcing him to be its 'angel of death', and there it is telling him he should do this and he must do that, and from Raz's perspective leaving out crucial information... and eventually threatening him. By the end he's calling it the enemy.
And maybe EG isn't the enemy, just this necessary thing... I was surprised myself that Raziel suddenly decides he's a big fat parasite. Then again, Raz is paranoid and pretty damn butthurt by the time EG became his 'benefactor', blames him for the physical state he's in and forcing him to live in his "vile carcass", and EG starts getting snippy in SR2 when Raziel doesn't do his bidding. Plus, Raz does seem pretty repulsed by its true appearance. Reminds me of the moment when he can't believe that the vampires roaming around the derelict Nosgoth could possibly be any relation to him and his brothers. Seems he would expect a real 'god' to look a little more aesthetically pleasing, he even insults the EG directly about its countenance more than once.
Gods and things with free will just don't mix, IMO.