The Thalmor and Empire both openly admit the concordat was just a stalling measure until the next war. The stormcloaks are fools who buy into passion over long term objectives and the eventually defeat of the Thalmor for nothing more then pride and belief.
Hammerfell sees it as both a betrayal and a surrender. Half of Skyrim sees it as a surrender. The current emperor will never again command respect after what he did. The Thalmor no longer fear or respect him.
It would be like the USA signing a peace treaty with the Nazis and..
A) no longer being able to worship God and
B) disbanding the Marines, the secret service, and the CIA (the Blades were a lot of things, elite soldiers, spies, and the emperor's honor guard) and
C) surrendering Texas to the Nazis, then Texas saying "[censored] this [censored]" and fighting their own war against the Nazis and kicking them out of Texas and
D) having Nazi embassies all over the states hunting down and murdering christians legally.
In this scenario, its like the West coast wanting to secede from the union to set everything back right.
The empire is the only thing stopping the Thalmor from ruling Tamriel. Weakening it by losing Skyrim only helps the Thalmor. The Thalmor even admit Ulfric is an asset to them, as you can read in the Thalmor Embassy.
The old empire was the only thing. This empire is a defeated empire. An empire which cannot defend its populous does not deserve to rule.
If the dragonborn chooses to aid the Stormcloaks, they will kick out both the Empire AND Thalmor, then rebuild Skyrim without Thalmor intervention, just like what is happening in Hammerfell.
Don't forget what the Stormcloaks' longterm goal is, the destruction of the Thalmor. Its not a question if Skyrim would aid the Empire against the Thalmor, it is a question will the Empire aid Skyrim against the Thalmor. The current Emperor is weak. Hammerfell has already lost faith in him. A strong High King of Skyrim will command respect among both Hammerfell and the Empire. Everyone in Tamriel knows the High King will never sign a peace treaty with the Thalmor.
The Empire are thalmor puppets you say? That's propaganda that applies to the average nord to help Ulfric in his quest for power. If you haven't, you need to learn of the Markarth Incident. Ulfric is openly racist, condemns the dunmer to the gray quarter, and doesn't even let argonians live in the city. Nords even tell he goes too far. He only helps Nords.
The concordat is just a stalling measure, this is openly admitted. The fools who compromise the strength of the empire, support the Thalmor.
Markarth Incident involved Ulfric's father according to Ulfric. Racism can be found all over Tamriel. Humans in TES lore are actually the least racist of all races. If you get hung up on that then why on earth would you support an empire bowing down before the Thalmor which literally intend to enslave the rest of the lower races just like the Alyaid did?
Stalling measure or not it was a great mistake. Titus II needs to die before the Empire will ever have a chance to recover its lost glory. Tiber Septim would be ashamed.