I think the thing to note here is that no one in-cabin realized the thing was stalling. The co-pilot noticed he lost the auto-pilot and wanted to (I assume) get out of the storm because it was freaking him out he probably didn't feel comfortable flying in it.
Surely as a private pilot you can understand the role distraction must have played here. I'm not licensed or anything but I have a measly 5 hours training in helicopters, one of the biggest things I start to understand is you either fly the instruments too much or you forget about them for too long.
This co-pilot's trying to keep himself and a hundred or so others alive, made the mistake of applying low-level techniques to a cruise altitude, and of course the miscommunication played a huge role as well.
Just my take anyway, interesting read.