As for Gilneas, she originally had no interest in it. When Garrosh swung by after her suicide in Edge of Night and forced the Forsaken to attack the Greymane Wall, however, the val'kyr gave her an out from the hellish afterlife she'd been thrust into: make a pact with them and they could return her to undeath at the cost of one of them, so long as at least one of them was still able to take her place in the afterlife (it took three of them to heal her at the end of Silverpine, however). When she returned to the front, she told Garrosh to fuck off after he tried to intimidate her--damn near laughed it off, even, and told him that compared to her afterlife, nothing he could do would ever intimidate her again--and began using the Forsaken far more conservatively than she had before, seeing them as a buffer between herself and her afterlife.
Awesome sig by Elyaan is awesome.
We have faced trials and danger, threats to our world and our way of life. And yet, we persevere. We are the Horde. We will not let anything break our spirits!"
Also, the reaction was not proportional. 1 commander questioned the order, so Garrosh threatened the entire race...
Go do silverpines opening quests followed by horde side SFK or the opening of gilneas for worgen. Shes got reason to go, hes the only horde leader at the time openly telling her what she is doing is "an abomination" and leaving korkron there to kill her and all her people if they step out of line.
That and the mana bomb probably made her second guess the blood elves which i think she always thought she could easily over power and maybe now shes seeing things more as blood elves on one side, worgen backed by the entire alliance on the other should things come down to it and they choose to deal with her like garrosh.
Shes backed into a political corner and has to make nice.
That is a very good point and one I hadn't thought of, OP.
Initially I had thought it was fully justified that she help the rebels - Garrosh has been nothing but a thorn in her side since the off (though I fail to believe that Thrall would actually have allowed her to do what she's doing for too long, even if he was, by comparison, a timid leader) - but now that you suggest that they'd be better off keeping out of it, I agree with you. They're working on some pretty dispicable things, and I'm sure Sylvanas would be more interested in progressing that than getting rid of Garrosh - unless of course she just has an intense personal dislike of him. Sylvanas is a very selfish individual, to some extents. She doesn't care all that much for her people, that much was clear after what she said when she tried to finally kill herself, and I think she cares little for the Horde as a whole. She's the sort of individual who does things because she wants to, because it pleases her. Perhaps she trusts the huge number of apothacaries to continue work on the plague (assuming they've not completed it yet) and feels that she can turn her hateful gaze towards the Warchief.
Personally, I love Sylvanas for those reasons, but I also wouldn't be surprised if, once Garrosh is dead, she did come under scrutiny. If the plague works - and I'm sure it will - she and the Undead will surely become a target sooner or later, by both Horde and Alliance. She only allied with the Horde through convenience, anyways, so I don't believe that there's that much to benefit either in the alliance for her or the rest of the Horde.