Ok so I caught 38 minutes a little while ago on Tv again and noticed something I didn't notice before. The Wraith goons at the begining of the episode damage a puddle jumper with stunner blasts.
This is actually what causes the pod to stick open and create the whole plot for the episode.
Thinking back to some more recent episodes it also seems like there's other cases of stunners doing something other than stunning. Look at Sateda for one where stunner blasts damage wooden boxes, or the flashbacks from the same episode where what looks like stunner blasts kill Ronon's squadmates.
If you look back to early season 1's "suspicion you'll also see McKay take a stunner in the face which prompts Beckett to talk a bit about how it works.
He says it's only designed to incapacite, but from the description he gives of how it actually works it seems like it would be ridiculously easy to make it kill someone.BECKETT: Your body experienced a full overload to its sensory and motor nervous system.
BECKETT (to Sheppard): It's really quite fascinating, actually. The Wraith weapon impedes the firing of neurons that enable the necessary ...
BECKETT: The paralysis is only temporary. Don't worry, Rodney. You'll be up and about in no time. (To Sheppard) Bloody good thing that Wraith weapon is only designed to incapacitate or he'd be dead.
It overloads the human nervous system and stops neurons from firing, but only in such a delicate and selective way as to immobilize the person as opposed to causing massive irrepairable brain damage or stopping hearts and other organ functions, all of which rely on the nervous system's connection to the brain to operate.
This of course is on top of the fact that it seems to be able to cause damage to a puddlejumper, which is obviously harder than McKay's face.
So I'm thinking here that Wraith stunners probably have some sort of power level setting or a variety of "modes" like a fire selector on a modern assault rifle. The stun mode is used most often, and probably represents the default setting, but there seems to be a way to make your stunner damage inanimate objects to. I also find it likely that the portion of the weapon that plays with the nervous system could be used to kill. It's just so extrodinarily difficult to make it "only" stun someone that way, that making it kill them through the same method would be trivial by comparison.