We were just talking about this in another thread...
Spoiler
I just learned that if you replace McNamara, then there is no peaceful path for the NCR and BoS. I got stuck on the Very Same quest, and broke with the NCR at that moment for giving me no more humane options. Apparently if McNamara is still in charge, a peaceful option is available. Way too late for me though..
Actually, I've heard it both ways. That if Hardin is in charge you can't form an alliance, but also that if Hardin is in charge and you do the follow up quest and join the Brotherhood you can convince him to make an alliance.
As for the OP: There is a bug that if you're doing both objectives for Hardin and McNamara and you turn in the final part to McNamara then tell Hardin the part about the Chain that Binds they bug out and no leadership is changed/can't do the follow up quests. They just sit there and say "I'm preparing for blah blah blah"