I only have clear recollections (or relatively clear, at least) through issue #49, but I really hope so. From what I've heard of Breaking Bad
post-season one (which is the only season I've seen so far), Bryan Cranston's character is pretty much considered irredeemable, and we've had other nicely dark and amoral characters on cable as well (Tony Soprano, Vic Mackey, etc.). From their track record so far, I don't think AMC would be too concerned about shying away from that sort of characterization, so I'd be interested in seeing how Darabont and company could pull it off.
Speaking of the issues, I recently borrowed two hardcovers from a friend in order to work on getting caught up. I have books five and six, so I'll get up to issue #72 through these, then get fully caught up with single issues.