The subtext of Emperor's story is that he's full of shit. He was mind controlling people like crazy including his 'partner', and there's no reason to think he was only eating badguy brains aside from his word.

It's open for interpretation how full of shit he was. He is evil human rather then an alien being.

As for the eating bad guy brains, I was talking about the other Illithid. I freaking hate that one. They just had to humanize the Illithid. They are now just poor victims of the elder brains rather then an evil alien race for whom we are food and less then bugs.