A united Empire has a much stronger chance of defeating the Dominion than a bunch of Nords with no one to back them up because they're all racist. They also will be weakend from the civil war so the Dominion can and will march right into Skyrim.
He also wants the Dominion out of Skyrim but he's too head strong to realise that if he wins the Empire won't be there to protect them. The Stormcloaks hate the Dominion and I get that but they're fighting the wrong people. The Empire AND Skyrim would have both lost in the Great War if the didn't sign that treaty.