I told the guy I would try to negotiate for a release but I get shot at as soon as the Khans see me. I am neutral with the Khans. I tried using the console to add a Khan outfit, and changing them to Idolized. Neither worked.
Any Idea why they are pissed? I should be able to get to the leader and talk.

What are you wearing?
Are you approaching them with your weapon drawn?
Do you toy around with the console much?
Mods?

Do not wear Khan or NCR's outfit when you negotiate with Khan at first place.

Just wear normal outfit.

Armored Vault 13 Suit
No weapon
Only when troubbleshooting, then I reload to before messing arround
Lots of mods, most are quest fixes. But it still happens when I disable them
Looking at the GECK I found that the "Negotiator" flag is only set if you tell the NCR guy outisde "I Understand" before entering the ruins.

However it dosent seems to change the attitude tward me.

I'm looking through the GECK looking for the trigger for them to attack but have yet to find it.

Your mods easily could have changed a value that persists across saves.

I went in Naked and Unarmed and it makes no difference. Setting the BoulderCityGreatKhans to Neutral also results in being attacked. Only setting them to Ally and Friendly works.

Looking over the topic scripts it seems when you talk to Monro he flags the quest as Negotiator but only sets the NCR to Ally, leaving the Khans as whatever they were. The Boulder City Great Khans have no default disposition with the player.

I http://www.newvegasnexus.com/downloads/file.php?id=37952 to resolve the issue.

You're the first person I've heard with this issue. Khans, in general, are non-hostile unless specifically set that way. You can be villified and still visit their home base peacefully. It probably became an issue with a mod you have.

Is Boone your follower? Boone doesn't particularly like the Great Khans.

Yeah, sounds like a mod/glitched save or general bug/glitch issue. Boone doesn't have anything to do with it, I've done that quest with him more than a few times.

Did you try reloading an older save and progressing to that point and see if it still happens?

What did you say to the NCR lieutenent outside?
If you told him that you're going to try to sneak out the hostages, the Khans are already hostile (well, they were for me when I tried that option)
If you tell him you're going to kill the Khans, you have to.

True. But none deal with Boulder of the Khans. If I could just find what events trigger the hiding Khans to come out of hiding then I may be able to track down the source of my issue.

Had the same problem and had to sneak/stealthboy to the headquarters.