Sorry, but I don't buy the retcon (which is what WCIII effectively was). Read the official lore on the Blizz site. According to that, the foothold the Legion has here was on account of the opening of the portal. Indeed, the opening of the Portal was a legion plot. Prior to that they were banished from the realm.

The Scourge are here because of a cult of orcs.

Judging by their own lore, the COT instances don't really work for the Alliance. One could perhaps argue the aiding of Thrall was necessary... the Orcs already being here, some sort of dual effort was necessary. The Opening of the Portal? Blizz contradicts their own lore on that one. We have to let the Legion plot to open the portal succeed in order to prevent the success of the Legion later? Don't think so.

The Alliance was badly damaged by the war, certain alliances were disrupted by the Horde races (remember the Belfs and Humans were once allied before the later troll wars).

As Varian said, who knows what the world would have been like if the Orcs had not come? I can't help but see it would have been for the better. Not because Orcs as they are now are necessarily evil, but because when they came, they destroyed and the situation of the Alliance is a state of recovery from what the Orcs did to them.

Yet we never see anything of the Orcs seeking to atone for the evil they did. On the other side, even the Internment camps could be seen as merciful: if you have a race of psychotics rampaging, you can either slaughter them or lock them up. The Alliance chose option #2

TL: DR, I think Blizz decided to whitewash the Horde and it looks real inconsistent to me.

Really, I cringe at how bad the rationale is for the Alliance. It's like Blizz designed these instances for the Horde POV and through in the Alliance reason to be involved as an afterthought

Wrynn is rather benign compared to the "Death to the Living" approach of the Forsaken. Moreover, when it comes to Wrynn and Garrosh, Wrynn is opposed to the Orcs because of what they did. Garrosh is of the opinion that these things of the past were a good thing.

It's a big difference.

Some Alliance may be racist, but the hatred and fear is not coming out of the blue, but from real evils done to the Alliance.