So, I have two points that no one has brought up yet, that may counter some of the arguments people have been making here. Reading The lesser Evil from The Last Wish seems to be the best context for this decision.
First, people say Geralt is neutral in principle. For the games, that depends how you've been playing him. He gets pretty involved in the politics in Witcher 2, depending on how you play out that story. So I have to assume people think Geralt is neutral due to how he is in the novels. I've read through all but the second half of the last novel now. In the novels, Geralt makes arguments for why he should stay neutral, it's true. It is explained that the 'witcher's code' is basically made up, and is a way for the witchers to decide how much they want to get involved. How much Geralt wants to get involved is a story arc within the novels. Around the end of Time of Contempt (I forget when exactly) Ciri is being passionate and indignant about Geralt hiding behind his neutality. For me, the arc concludes with him changing his values and deciding it's worth getting involved sometimes. Maybe not when there is no right choice, like with the conflict between the elves and the humans in the first game, but other times it is worth it. That's why for me Geralt decides, in Dijkstra's words, not to "ride the current to hell" and actually help kill Radovid.
Now the second point is about the choice between Roche and Dijkstra. Some people have made some very good arguments for both sides, so I'll try to say only what I don't think has been taken into account. I believe that Dijkstra isn't wrong in what he is doing. I also believe that if Roche 'n' Co were to surrender to Dij, Dij would either imprison them, or exile them. They do know Dij was behind the assassination, which is a problem for Dij. Either way, the Temerian patriots are too patriotic, and would fight to the last man regardless. Geralt is not a Temerian patriot, to my mind. This is where I believe he would draw the line for fighting for Roche. He would do a lot to save these people, they have had his back and he respects them. Same goes for dijkstra I think. It's a fight between two friends. That being said I don't believe Geralt forms friendships that fast. More I would say they are all allies he respects. I don't think he would feel obliged to fight for Roche n co when they aren't fighting for their lives, but instead are fighting entirely out of patriotic fervour. End of points I don't think have been taken into account.
I believe Geralt is very much for a plan that will hold off Nilfguaardian slavery and imperialism. I love Thaler. He's like my favourite character in the whole 3 games and all the books. I respect Roche and Ves, though they are a bit stupid I reckon. Not unintelligent, just stupidly dedicated to their country. If I could see one thing changed about this game, it would be that Thaler is imprisoned or exiled instead of killed. I believe he is enough of a pragmatist to see a bigger picture. Roche and Ves of course would still die valiantly fighting for (dead) king and country. Either way, I choose not to try to save the poor brave patriots.