While aliens were not actively sought out, and indeed actively discriminated against in the Empire, the Empire still respected excellence. Those with enough power or skill, regardless of species, were able to take part in the Empire. That being said, it would take a lot more effort from a non-human to make any sort of progress therein, but it was possible.
How many alien types were accepted into the empire at this time period. I dont know the TOR lore at all.