Not sure if you've figured this out yet, but after you first talk to Danse in the bunker and he says he's going to leave the Commonwealth (after the charisma check), you have to leave the bunker. You and Danse will be confronted by Maxson, where you have to pass another charisma check to get Maxson to spare Danse. After that, Danse will be available as a companion, however the Brotherhood will be hostile whenever he's with you. You can kill un-named BoS members and not lose points with them when he's with you. It should also be noted that it's impossible to max his affection and gain his perk until AFTER completing Blind Betrayal.