After the Siege, Garrosh is dead and stuff, but can that really be considered an end to it? I think not. The Pandaria campaign was very bitter, and it's without dispute that while Garrosh ordered the atrocities at Theramore, Southshore and Gilneas, so much of the Horde was complicit and actively involved in these that you can't just consider it over and done with with his death. The Blood Elves and Goblins in particular have a lot to answer for in Theramore, the Forsaken in Gilneas and Southshore.
Further, it's suggested that Sylvannas raises Alliance troops to fight for the Forsaken during the Siege which is pretty reprehensible.
The recovery of Y'Shaarj too was spearheaded by the Reliquary and Goblins, again 'acting under orders' isn't much of a defense. If Garrosh knew what it was capable of, then it's ridiculous to suggest the Blood Elves especially didn't know, or hadn't figured it out. It's not like Garrosh really made much of a secret of what he had in mind in terms of weaponising it anyway. Still, they went on and recovered it.
I'm just not sure how relations could be normalised so quickly after such a bitter conflict, regardless of whos put in charge, because each of the Horde's factions' leaders is still guilty of at the very least complicity of some of the more terrible acts - Lor'themar, Gallywix and Sylvannas especially, but even Baine was at the forefront of the initial assault on Theramore. Even a change of Warchief to someone with a "freer" pass, like Thrall or Vol'jin wouldn't change or make up for what they did.