If the GM builds certain sorts of moral evaluations into the gameworld - such as that extrajudicial killing is in some circumstances morally permissible - and then has players who arc up against that, I think the GM has run into a problem that was entirely forseeable. If the GM isn't prepared to feel this stuff out gently and see how it plays, and instead wants simply to run roughshod over the moral sensibilities of other participants in the game, then I don't have much sympathy if conflicts at the table are the consequence.
In this sort of game, if I started a series of violent attacks upon the slave owners, and the GM started hosing my PC as a consequence, I would be irritiated to say the least. (There are framing issues here, like compromise among players in the interests of party play and the like. I'm assuming that that sort of stuff is under control). I expect a GM to accomodate my conception of my PC and his/her exploits, and as a GM I do the same for my players. Doubly so when it comes to the moral and evaluative dimension.
I don't really feel the force of this analogy. The GM is nothing like the national government of the US or any other state. Even if I don't like the norms that the government institutionalises by way of law, I will be obliged to comply by the apparatus of enforcement and administration that the government has established. At least in a country like the US, for most people their lives are intimately enmeshed in that apparatus.
Whereas the GM is just another person sitting at the table. If I object to the norms she is trying to operationalise in the game, I can say so. And not unreasonably - I'm here to play a game. Why should I have to subordinate my moral sense to hers in order to do that?
No. I'm suggesting that, in the course of play, it has turned out that some (one?) player(s) don't like the moral situation the GM has set up in her world.
This isn't an issue of GM authority in the abstract. Nor is it, as far as I can see, about the fact that the players promised to play in the game that the GM pitched to them. As you yourself say, in the course of play it has turned out that some players don't like at least some part of that game. And not, as far as I can tell, for some frivolous reason, but for some sort of at least moderately deep evaluative reason.
Any sort of promise to enjoy the GM's game strikes me as largely non-binding, given that we're talking about a leisure activity. And doubly so when it turns out that the player can't keep the promise because of a sincere moral viewpoint.
Sure there's a difference. But any game which includes alignment mechanics is asking for this problem to arise (it's why I think alignment mechanics are, in general, unnecessary and a recipe for conflict among participants in the game). I mean, Linda is saying that she and Mark know better than Sean what is good or bad. And Sean, not unreasonably, doesn't agree. Telling Sean that he promised to obey Linda on this point two or ten or twenty weeks ago is neither here nor there - he promised to let her GM the game, but not to be an authoritative determiner of right and wrong (it's not even clear that such a promise would make sense).
Unless I'm misundertanding, though, the GM is setting parameters on how you may play your PC if you want to be counted as good. Which seems to be the issue.
It seems to me that they want the play of the game to reflect, at least in part or to some extent, their own moral conception of their PCs' actions and circumstances. It strikes me as a concern not about the status of their PCs, but about their status as participants in the game.
Yes. But that the problem might arise strikes me as highly predictable. And a GM who assumes that the problem can be resolved by pointing out to the players that they agreed to play in the game strikes me as not really understanding the core of the problem - which is that you can invite someone to entertain the idea that what they think is wrong is really right, but in the end it is hard to make them stomach it.
I think there is a fairly obvious path to a possible solution - stop making the controversial stuff the focus of play, and to the extent that the players bring it up themselves, let them sort it out while remaining neutral as GM and doing your best to steer play towards other matters. Whereas rubbing one or more players' noses in the fact that they don't like the moral set up strikes me as just a recipe for more conflict.