Imperius doesn't hate the nephalem but only hates the demons. He's ok with what Malthael is doing because all Malthael tried was to capture all demonic stuff into the black soulstone which would kill all nephalem as collateral damage. Imperius doesn't like the nephalem but killing them doesn't fit him because they are partially angels. Imperius helps us only because Malthael attacked the high heavens to gain access to pandemonium.
Nobody wanted to kill the nephalem but to capture and destroy the demons. As long as the nephalem don't go crazy and attack the high heavens the angels will do nothing. They already voted if they destroy the nephalem or not and decided to not kill them and that's what they will do. On the other hand they also won't help the nephalem and Tyrael was the only one who helped us against the demons. Imperius didn't care that Belial and Azmodan tried to get the black soulstone to become the prime evil because it only affected sanctuary at first.
If they do a branching storyline Imperius could be a boss if you choose to side with the demons but apart from that. He isn't a bad angel like many people see him but he's simple and extreme in his thinking. All demon related is bad and needs to be destroyed and everything that was decided by the council is the right thing to do to maintain order.