It seems like the story is going to progress through Mists of Pandaria that Garrosh is going to come increasingly under the influence of a mysterious entity called the Sha. These creatures gain strength from negative emotions, such as doubt, and use that strength to corrupt those around them. Eventually, Garrosh is going to cross a threshhold, possibly the destruction of Theramore, possibly something hitting closer to home, such as the murder of Varok Saurfang, that will convince Thrall that it is time to remove Garrosh from the throne. That's the Horde side of the raid, the Alliance side is pretty much that they finally figure out that they're at war. I have a lot of issues with that set up, but I'll save those for when we have more information, or I'm particularly bored. The biggest fears at the moment are with regards to how the event itself will be handled and how the aftermath will go down.
Alliance players are afraid that this is going to be a rehash of the second half of Cataclysm, where it's nothing but "Save Thrall from his own angst!" and "Help Thrall become the Earth Warder!" and Alliance players are wondering why they're helping their sworn enemy. If the raid devolves into "Help Thrall defeat Garrosh!" for Alliance players, then it would be, as I said earlier, the death knell for the Alliance as a interesting faction, they'd be nothing more than foils to help propel Green Jesus to greater glory. It's an incredibly demoralizing prospect.
At the same time, Horde players are understandably upset at the prospect of an Alliance army, led by King Wrynn, smashing down the gates of their capitol city and butchering their leader. If an opponent can take your capitol and decapitate your leadership, then your nation is a step away from the dustbin of history. Spinks was worried that it could herald the annexation of the Horde into the Alliance in order to facilitate cross faction grouping in the expansion afterwards. While I find that notion unlikely, the fear of losing their unique perspective within the game is a very primal one.
Blizzard is walking the razor's edge here, and they don't even have a good reason for it. But I have some advice for them as to how they can avoid catastrophic alienation of either factions.
The first step, and admitedly, the most unlikely, is to scratch Thrall from the story. Either just put him on the first bus to Nagrand so he can raise his oddly colored children in peace, or, my personal favorite, have Garrosh kill him as the catalyst for the Horde players to rise up against him. Whatever you do, don't just put him back as Warchief and then carry on as if nothing happened. Doing that exposes Garrosh as nothing more than a cheap plot device to create the war that allows Thrall to come back as the messianic peacekeeper. The Horde then gets to deflect all the blame onto Garrosh, completely undermining any analysis of the foundation that the Horde is built upon. At its core, this path is tantamount to retconning away everything the Horde has done in Cataclysm. Nothing that happened would matter because it was "Garrosh's Horde".
Regardless of weather they keep with the decision to use Thrall as Garrosh's successor, or someone else, there's another thing that they need to keep in mind, faction segregation. Do not have the Alliance following the Horde leader around again. Do not have Horde players following King Wrynn around. You can have them meet up in an ICC gunship or ToC faction champs fight, but don't make them feel subordinate to the opposing faction. That's a recipe for discontent. Both factions need their own reasons for pushing after Garrosh, and their reasons have to be driving force within their instance.
One final tip. Do not make the impetus for Horde action be that Jaina went and cried to Thrall after the Horde smashes Theramore. That'll just piss everyone off.
As far as to how the Alliance is going to be convinced not to simply crush the Horde under its boot after they storm the streets of Orgrimmar, you're on your own there Blizz. I warned you this would be coming, and you really don't have a way out that doesn't involve some ridiculously hack writing.