Glad he left. Movie would have set his career back another two years. He's already gone through that before.
how would this have hurt his career? christopher nolan did a "comic book movie" and it was probably the biggest thing to happen to his career. he went from being a talented but relatively unknown director to the a-list. he definitely wouldn't have had to scope and means to create something like inception if he hadn't had dark knight under his belt.
of course.... this is all assuming that the aronofsky wolverine would have been a quality movie on par with dark knight (in terms of comic book movies) as well as aronofsky's other work.
the main worry was that Fox would intervene and try to take over creative control. however, the beauty of aronofsky directing this was that he has a lot of influence and pull over at fox since he's given them recent hits for their indie label fox searchlight (black swan, the wrestler)