Yea while your in the High Heavens he tells you through the story that Malthael has become sick and he doesn't have the heart to kill him. So the task falls to you. As more and more Nephalem start to be born I'm sure the angels would have a contingency plan of some sort. I'm sure that since being a Nephalem you have an equal part of both angel and demon that full on corruption isn't possible without losing some of the strength of the otherside.
Also Malthael didn't attack the High heavens to gain access to Pandemonium, he had been there from some time. The fortress had twisted it self to his thoughts over time. It's not like you could walk in and BAM it changes hogwarts style.
Actually from what I've read from the book of tyrael, The entire council at least respected Malthael. Since he was the voice of wisdom they would always stop their bickering and listen when he spoke most often following his suggestion. As far as Imperius hating us and wanting to destroy us, his code of valor would never allow him to use the blacksoul stone and all of the evils captured in it to kill us. He might hate us but he hates the creatures of the burning hells even more. While your playing act 5 you get to talk to Imperius for a moment and he gives you an explanation of why he's willing to help.