I want to complete this quest without destroying the Hidden Valley bunker, and
it states in the game wiki that after successfully completing the "Still in the dark"
quest a truce can occur with NCR.
I completed Still in the dark gaining a "liked" reputation with BoS (McNamara is
still in charge) and got him to end the lockdown. The only dialog I can have with
McNamara now regarding NCR is how the NCR wants to destroy him.
Is there anyway now to end Moore's quest without having Veronica run off?

The wiki is wrong, I believe. You have to do Eyesight to the Blind, not just Still in the Dark. I can't confirm that 100% though. Eyesight to the Blind is what will lead to you becoming a Paladin and I would presume that's what you need to get the truce.

Thanks, I'll try that.

Wiki is correct.

You just have to finish the first part of the quest.

After you finish, McNarem(sp) will tell you he is busy lifting the lock down and you can come back later.

When I came back I got the option to talk to him about NCR, and he said he is willing to cooperate with them. In exchange he will allow Paladin to help against Legion - so consider what NCR is facing they wouldn't turn it down.

He is right.

When you go back and talk to the Colonel in Hoover Dam, she said she doesn't like it, Brotherhood svcks, but she did accept it.

After that I went back and asked to "Join the Brotherhood" and that started the Eyesight to the Blind Quest (the one with Black Mountain).

[Edit]

I did however finish Veronica's Quests and the Brotherhood side quests (Lost Pistol) prior to this. So I am not sure if that has anything to do with it. It might be a reputation with the Brotherhood thing.