You are right, although it's a lot less likely then this current type of very nasty yet very passive crime. Your scenario requires the perp to commit another crime and it's a crime of a very different nature - visceral, physical and in this context likely very personal as the cockpit victim will also be a colleague.
However, with so many flights, pilots and aircrew operating in budget air space and pilots increasingly looking like interns paying for their own training, it's impossible to discount your scenario. Given time, it will happen, basically. If it can, it will.
All this of course takes place in a context of a massive reduction in risk to passengers in commercial flight. These events are, every time, examples of "availability bias" in human decision making.
The most intriguing part of this, for me, is to what extent this event will foster debate on fully autonomous computer flight systems and remote cockpits. I think we will soon see pilots at the front of the plane removed of final authority to command the aircraft controls. The fact that this is technologically available now, practically off the shelf in a hardware store, makes this, for me, an absolute certainty.