Bottom line, keep the autopilot on during high altitude over speeds. You are more likely to just get yourself into trouble with inappropriate pitch inputs that were not necessary anyways. Just accept the overspeed, realize that it not dangerous, maybe use some speedbrake and then write it up as appropriate.
As for the faulty AoA concern, alpha prot strip increase is a slowly increasing value as Mach slowly increases because the AoA vanes are stuck in place instead of slowly moving toward what I will call the cruise altitude position. This particular event appears to be a sudden increase in the alpha prot strip likely due to some g-loading in turbulence causing vane movement. I suppose one wants to recognize the difference between g-induced alpha prot strip increase and stuck vane increase in alpha prot strip (recognize the circumstances likely to produce both).