When you explain it like that I have to say it's not as "moraly ambigious" as it seems. Really, this is nothing new and has actually historical examples in real life. Concentration camps and the medical testing which happend there. But it also happend in the Soviet Union and some Gulags.
Is it acceptable to let some people suffer when you can get a cure or medical knowledge that could cure people? And the overwhelming majority of medical experts says cleary, no it isn't.
Bethesda really does suck when it comes to "choices". Because to them it's all binary. It requires good writing. And that's something they simply lack. When you really look at it "moraly grey" choices doesn't come from putting the player in a place where he HAS to make a choice. It actually comes from the characters you encounter. Want a good example? Mr. House and the NCR. I prefer the NCR, but I can see where house is coming from. He's not evil and the NCR is not goodö. They represent view points. Ideas how New Vegas should be ruled. It's the interaction with the charaters here which makes it moraly grey. You either agree or disagree with them. But you can not say that House has less claim over Vegas than the NCR. Or that the NCR has no right to be there. Even House sees the need to have them as trading partners for example. And this is how you crate some moral ambiguity. By creating debth and have some decent writing.