There seems to be no way to end the conflict between NCR and BoS peacefully, assuming you support Hardin as elder. He gives you a key to the safehouse and then sends you on your way, but the NCR quest still lists 'find a way to deal with the brotherhood' and the only way to earn their trust is to wipe them out. This is despite the fact that there's a dialogue option with Cassandra Moore regarding a possibility to defuse the situation diplomatically.

I haven't tried completing the quest with the previous elder, and unfortunately can't due to having saved over that part of the game, but as far as Hardin goes, you can't ask him to quash the beef with the NCR. Right now the only way I can proceed with the main quest for the NCR is to blow up the bunker or kill everyone inside.

Just to confirm...

Ugh. I was afraid that was the case.

If ANYBODY sees this thread and has an idea as to how to solve this without reloading a save from bloody 10 hours ago I would greatly greatly appreciate it. It feels like a game-breaking bug to me . Maybe there is a console command to revert only McNamara to his previous state and maybe trick the game into thinking you have truced with Hardin?
In my opinion there is no reason as to why Hardin would NOT truce and therefore it is most likely a bug...

Well I found this console command from Fallout 3.
setally (0/1 optional) (0/1 optional) - sets a faction as an ally with another specified faction. 0=Ally 1=Friend.
and the faction ID for the Brotherhood of Steel is 0001D3FE and 000A46E7 for the NCR (i think) but using the command doesn't seem to do anything.
Maybe somebody knows how to use it correctly for New Vegas?
Again... any help would be much appreciated

I don't know if that would work as it's more of a quest problem.
If we're going with console commands (I have the same problem) what we need is a way to activate a part of a quest or skip to the next step in a questline. Basically, I figure that aside from a patch, the easiest way to fix it will be to somehow jump to the next part after "convincing" the brotherhood. EIther that or find out what the value is for Macnammara that cuts off that dialogue and then change it. The problem for me isn't that the dialogue doesn't appear, but that there are no dialogue options with him now. I try to talk to him and he says a line about having to deal with the charges but that's it and no speach window opens up.

You need to keep the old elder in place to save BoS from the NCR blow up the bunker mission. Siding with the head paladin results in BoS's Doom since he will stick to their code of conduct even to the bitter end. I had to go back in alot of saves to save the BoS when I did my NCR loving run.