A friends having a nitemare taking off a rear wheel. All I know, is that its a kona stinky, with a bolt through rear hub.

Is there anything out of the norm he should be doing to get it off?

I have a Faith with a rear bolt through and I have to completely remove the axle locking nut so that I can remove the wheel – otherwise it gets jammed up in the rear mech and can't be removed without bending the mech hanger.
Might be something similar on a stinky.