Until Maxon tasks me with an Arthas-style culling of Stratholm upon Good Neighbor's sentient populace, I'm going to say he is aware and has *some* level of tolerance for individuals of sentient and peaceable existences in the wasteland. Blind Betrayal doesn't count as you can convince him otherwise to spare Danse, and he doesn't undermine your wishes by having him killed some other way. Which he very well could have.
Now, unlike some other chapters of the Brotherhood, he would never allow a ghoul, or super mutant, or Synth to actively serve under his command. Is it racist? Sure. But the Brotherhood's Bigotry isn't just some war between socioeconomic classes of humanity. It's about protecting themselves from what has proven time and time again to be an active threat. As sad as it was, Danse really had to be banished as the alternative. All it would take is the institute to find out he was N-7 9-7, for them to issue a recall code and learn *everything* Danse knows about the Brotherhood, secrets, weakness's, relationships. Or even worse, reprogram him to know all these things and set him out against the Brotherhood.
Between that and the feelings of utter betrayal people had accrued from learning he had been *hiding amongst them* It just wouldn't be safe for him to be with the Prydwen crew anymore. Not while they were in a war against the institute, not after he had run away and made himself to appear traitorous.