The easiest solution is to ask each player to make a character who already wants to defeat Ragesia. Barring that, I would ask each player to come up with a reason why they want to get to Seaquen, and hope that by the time they get there, they've got a dislike of the Ragesians and want to fight back.
Maybe they are a mage and want to avoid the Ragesian scourge, and they see Seaquen as a safe haven. Maybe they actively want to join the resistance to fight Ragesia. Maybe they're planning to be a spy for the Ragesians. Maybe a sibling or lover fled there first and they're going to protect her. Or they might already be a student from Seaquen who was in Gate Pass on a different mission and wants to get back quickly.
Also, play up the fact that the Ragesians are able to cover most of the paths between Gate Pass and Seaquen, so that the best hope is to take the somewhat dangerous but not heavily-guarded mountain road to Innenotdar. There is the option that they might try to team up with the Shahalesti and avoid Innenotdar by going through the elvish nation, which would result in skipping adventure 2, but as long as each PC has a reason to want to go to Seaquen, you can pick back up with the rest of the campaign saga, and maybe retool adventure 2 for inclusion somewhere later.
I'm curious, Chimera, what sorts of things you thought the module was too restrictive on. I admit, it was my first written module, and if I could redo it, I'd want to loosen it up a bit. Maybe adventure 2 too.