So aren't those Star Wars petitions worse because they call for a reverting of the changes Lucas made that occur throughout an entire movie that are even more relatively incidental?
It's hard to say, I think both versions of all three films are basically garbage, and people want them restored because of nostalgia, not some objective sense of the film having been made weaker as a result of the changes.
Films are not beyond being heavily altered of course, Blade Runner is a good example, there are quite a few distinctly different cuts, including heavily altered versions of the ending. 'Final Cut', which is now generally considered to be definitive, ends with Deckard suspecting he is a replicant, and contemplating how long he has with Rachel. The original theatrical cut didn't feature the infamous unicorn scene, and ends Deckard and Rachel driving off with only her shortened life expectancy being his concern.
It's a radically different ending, one of them is as the director wanted, one is how the director was willing to compromise for Warner. I do think a similar situation could justify the calls for the ending to be changed with Mass Effect 3. If Hudson announced that EA had pressured the studio to have the ending it does, and he had different plans, and thanks to the outcry is now going to implement his original intent, that's fine. However, if it's just a case of the audience not liking the ending, so they're folding under pressure, I think it's shameful to change it.
Of all the things I dislike about the ending, there is no question they had a specific idea, and ran with it. There's reason to believe they wanted the controversy, just didn't expect it to be this demanding, and while I don't personally like that concept, it is their work, to do with it what they wish.
If Kojima came out and said MGS4 is getting DLC, and they are restoring his original intent for the ending, I would be pleased, because that's what should have happened had he been given the freedom he should have. Mass Effect 3 is not that situation, they wanted this to happen, and it's backfired on them, but changing it is just pandering. Even more so that it's the end of a trilogy.
EDIT: And the charity element is completely irrelevant. People could have decided to give to charity anyway. It's almost worse than paying for a new ending directly because it's a bad PR situation if they don't, and bordering on emotional black mail. I wouldn't support it any more than I'd support Apple giving a hundred billion dollars to charity in exchange for the Mona Lisa having a hat added.