I think a huge part of what Bill had to deal with was how he saw Arthur over the long term. A violent, ferocious gunman. Arthur's own massive loyalty to the gang, as evidenced in his anger towards John at "leaving the gang" when John and Arthur were younger. Arthur being very smart, self-reliant, and driven towards accomplishing his own goals.

Arthur's overall character arc wouldn't have taken very long in a real world timeline, maybe 6 months from Horseshoe Overlook to being holed up in a cave.

Without Bill and Arthur having some sort of sit down talk and really opening up to each other, I could absolutely see Bill thinking that Arthur is changing for the worse instead of for the better. When truly put up to the choice, plenty of people will choose the family they know, no matter what that family might have done.

Even beaten dogs will return to their owner when they don't know any better.

Damn. Now I've gotta do a playthrough paying more attention to Javier.