But thats the thing hes not relivent for the first part or the second, so I dont see why it should insta fail, fail the last part fine, but not the first. I can kill a certain guy in the main factions life goes on...
I wonder if I can kill him before the uck 38 resets rep.
Think of it this way, because it's all the same quest... you're walking around the wastes and you find a key, completely unaware of what the key is for... and you decide to throw it in the lake (if that were possible). Later on, you walk through a huge cave, it's like 6 levels, at the end you kill the biggest Deathclaw ever, it's a Deathclaw Behemoth... and then at the end there's a locked door, behind that door is... whatever would end the quest... but you tossed the key in the lake, which someone would have told you about the location of that key and its purpose had you talked to them prior. You can't finish the quest.
Wouldn't you rather know that you can't finish the quest before you bother? The idea is supposed to be that you went through that, and by killing Motor Runner you basically tossed the key in the lake.
If that anology doesn't work for you... then just think of it as a "choosing sides" quest. You either help out the Khan by doing whatever, or help out the NCR. I think there's a way to do both, but they just have to be done in order. I don't think it's really a bug... just more a byproduct of open world gameplay vs linear games.