Eh. You really seem to gloss over a lot of factors.
The Alliance really isn't halted in PvP compared to Horde, other than Undead and Tauren Racials being the best, for sure. But that very Tauren HP racial is also a good benefit in PvE. (But don't forget Dwarves have Stoneform, which is amazing against Rogues or Warriors)
But if you're talking about PvP. Then Alliance have Paladins, who are by far the best healers in PvP. By a million miles in WSG especially.
The fact that they wear plate, a shield, and have bubbles, blessing of freedom, lay on hands and blessings - those spells alone make them outclass any other healer in PvP by a mile.
Engineering Holy Paladins are almost impossible to taken down in PvP.
So really with Paladins in your party I'd argue that Alliance should have a much easier time when in a premade to win WSG.
And again, for the PvE side, it isn't so black and white like you say it is. Just because Alliance have Paladins, and Fear Ward, doesn't automatically make you the best PvE faction in everything ever.
Vanilla WoW is balanced between the Horde and Alliance classes: The Shaman and the Paladin.
Both of them are hybrids, and both of them are usually just healers in raids. And if not, they're trying to rely on RNG to 1 shot people in PvP (Windfury = Seal of Command / Reckoning).
They both have extremely similar spells and effects, but each one in a slightly different way and manners.
Paladins use blessings, while Shamans use totems. That is the main difference of the classes.
Paladins are thus much more self sufficient because they also wear plate and have bubbles and don't have to rely on totem pulses to help themselves rid off enemy spells or debuffs.
But instead of self sufficiency, Shamans have more offensive utility spells such as the 6 second cooldown shocks (5 sec with talent) which is an amazing tool to interrupt and annoy other casters to no end, as well as kiting melee forever who are not being hand of freedom'd by a Paladin.
And then there's the infamous purge, having no cooldown and a low mana cost. Removing any buff or effect you could ever hope to use.
But there are spells here and there that they have, that the counterpart has none of.
A good example of that is Tremor Totem for Shamans. It is absolutely amaaaazing for Onyxia, as an example. And makes phase 3 considerably easier for Horde than the Alliance.
It's also very good on Magmadar, and really any PvE content with multiple fears, really.
And Shamans also have Windfury Totem. So if you're a melee dps raider, then you'd rather want to be on the Horde side, because your dps would be even more crazy with Windfury.
Paladins have none of that in PvE, instead they have more passive boosting blessings, and judgements to help heal the people swinging at the boss, which again, is a more sufficiency and sustainable playstyle over the more aggressive playstyle of Shaman spells.
Really the two hybrids of the Horde and Alliance were obviously balanced with such a design in mind.The PvE and PvP between Alliance and Horde isn't just black, and white. Really. It isn't.
And if anything, I wouldn't be surprised if Alliance win way more WSGs than Horde, as long as they premade and take Holy Paladins with themselves, it should never be an issue.
And I wouldn't be surprised if Horde down Onyxia before Alliance. It goes both ways.
