For the story they told, I think it was fine. They left out the whole thing about Stephen being a spy (although you could read a couple of things as hints, and Jack doesn't know for a long time in the books anyway), but there's plenty of good interaction between Crowe & Bettany. I think they hit just the right note with their portrayal of the friendship.

Definitely read the books if you haven't done so! I cracked up every time Killick said anything in the movie because he was so perfectly the character from the books.