I sided with Roche because, as firmly bashed over the head through all of Witcher 2, 99.9% of the people from the North are bastards so anything that annoys them gets my seal of approval. I was sad to see Dijkstra bite the dust or rather get chopped right in half during the fight but Emhyr proved himself the smartest and least dickish of the three choices for control over the North.I stated over in the Imperialism thread that there's really no choice for the "Old World" as Change or Die is a theme of the Witcher series, both games and books. If The North wins, it becomes a Redanian-led modernized industrial state which is almost identical to Nilfgaard. It may burn witches and have a state religion but, either way, it's modernized.
Still, I choose Dijkstra by inaction. I didn't WANT the Citadel Council to die but I did let them die so to speak.
In the end, Geralt couldn't get behind any treaty with Nilfgaard which let them have the South North. He also wasn't about to get involved in a fight between Dijkstra and Roche.
So he just left.