Is there any peaceful way to resolve the situation between NCR and the Brotherhood in this quest? I'd rather not kill off the Brotherhood. Thanks.

Depends. Did you make Hardin the new Elder? Hardin will never support the NCR. If you left McNamara around, however, he will join the NCR assuming you've completed the In the Dark questline.

Okay, cool. How long does it take for McNamara to get past the 'I need to prepare' dialogue thingy?

Simply leave Bunker L2 and then return, that will initiate the new dialogue sequences.

Okay, thanks, I did it.

Meanwhile I am sitting here all alone cause Hardin hates NCR or a glitch or something...