Yes indeed there are a few aliens that have risen high, but have you ever heard of an alien general in the imperial army? From experience the highest rank ive seen on an alien in the Imperial military is the chiss lieutenant turned major on hoth( presuming you give good feedback about him), even so if their are indeed aliens in the the higher echelons of imperial military their few number and the hostility from other moffs against them would put them in the lowest parts of planning operations. When it comes to he dark council by the end of of SW or SI storyline it seemed like everyone in the council was killing each other and bidding for power (eg: Thanaton,Baras) looking through the IA line Darth Jadus betrayed the Emperor and council while his daughter was punished by her fellow council members(eventually killed if you side with jadus). Just from this it seems like killing's and betrayal in the council are so often it is remarkable how they function.