I seem to recall you having this same problem before lol.
The Stormcloaks aren't really that racist, they just have a Skyrim first view of things. I think canonically, Bethesda will either say that the Dragonborn sided with the Stormcloaks, or use a Dragon Break to explain what happens, resulting in both sides winning and losing. Come to think of it, a Dragon Break could be very beneficial to stopping the Thalmor. Wouldn't the Thalmor crap themselves if they woke up one day and Skyrim was under Stormcloak control, with no losses on either side! I think that would be hilarious.
Anywho, take my advice for what you will. I see the Stormcloaks as the lesser of two evils, or rather, I guess you could call them the greater of two goods. Neither side is perfectly blameless, but I feel the Stormcloak's cause is more just. The Imperials are good people, but so are the Stormcloaks. Both factions seek to solve the same problem. One faction seeks to solve it by waiting, and being passive and submissive until the right time, whenever that may be. The other side seeks to solve it through fierce independence.
On the one hand, the Stormcloak plan is risky. Who knows if the Thalmor can actually be defeated in a military engagement. Last time an Aldmeri Dominion was broken, it was by Talos using Numidium. It's possible that without a similar leader, and a powerful trump card, that any efforts against the Thalmor will fail.
On the other hand, there's no end in sight with the Empire's "plan". Who knows if that day will actually come, and even if it does, will the Imperial Legion be ready for it? Who will they rally behind? Who will be the person that steps up and says, let's kick some ass. It certainly won't be any random figurehead Emperor that is chosen, now that Titus Mede is dead. Not to mention he was a spineless fool to begin with.
I see the Stormcloaks having the greatest chance for success, because they already have the two things I listed as a requirement. The Dragonborn would make a fine leader, way better than Ulfric imo. Someone with dragon blood and a real claim to the throne, the savior of the world, someone that's fought the Thalmor and won. The Dragonborn would be the perfect one to rally behind, in that regard he's probably better than the mortal hero Tiber Septim.
As for the trump card, the Dragonborn already possesses that too. He has the allegiance of Odahviing, and quite possibly all dragons after the defeat of Alduin. Too bad Paarthurnax is teaching the dragons his pacifistic way of the... oh wait. Canonically, all quests happen except for the mutually ones. This includes the Blades minor faction quests, as the greybeards quests can be done before slaying Paarthurnax. In other words, I guarantee he dies canonically, unless Bethesda saves him with a Dragon Break of course.
So the Dragonborn could potentially lead the Stormcloaks, and use the dragons as a weapon of war, his Numidium, to crush the Thalmor. That's my take on it anyway. Sorry that got a little long winded, I tend to rant about these sorts of things.