Ok, here's the deal...
I've done these things for the Brotherhood so far:
Got the holotapes.
Spoke to Hardin
Got rid of the virus (bloody annoying)
Spoke to security guy and found the restricted info to get the Elder out from his position. Spoke to Hardin and he was now Elder.
Got the missing laser pistol from the Scorpion place.

I got McNamara fired before I done the quest to find the scouts in the certain areas. Does that mean I can't get the Brotherhood on my side?

Cheers

Yes, only McNamara is willing to have a truce with the NCR , and you can't become idolized if you put Hardin in charge. You can more reputation for finishing the quest in McNarmara's favor then for Hardin.

Yeah you should have finished the find the scouts quest, then talked to Elder McNarmara, he would remove the lockdown and later you can make a treaty with the NCR and the Brotherhood. he would have also made you a member of the brotherhood