I think it's more than people just not perceiving the sword as a dangerous weapon, some people just don't want to view Duncan as maybe not being morally upstanding. It seems out of character, because overall, he seems like a kind, honorable and courageous individual. You can almost envision Duncan as being some great hero or icon... but he's a Grey Warden personified in the flesh, and he does what is necessary not what is right.
I don't think Jory could have even turned away before the Joining. I think he was doomed the moment he volunteered. If the PC refuses to join the Grey Wardens when Duncan attempts to recruit him, then Duncan invokes the right of Conscription. He apologizes and does it all in his nice seeming way, the same "I'm sorry" way he stabs Jory, but in the end he makes it clear that the PC has no choice.
From Duncan's point of view there is a Blight, and someone he knows is going to stop it. It might be one of the three recruits he managed to find. He's correct in all of that. There are only a handful of Grey Wardens nearby, and after Ostigar there are only two. Had Duncan let Jory walk away, what would have been the logical response from the PC? Who would want to willingly drink Darkspawn blood knowing they could end up dead like Daveth?
Duncan's killing Jory and making it clear that there was no way out, is effectively what ended the Blight and saved the Kingdom. Had Jory turned and walked away, the PC might have followed. The entire game, from beginning to end, proves that Duncan's actions were necessary. People want to argue what Duncan did was bad, mean, cruel, heartless, evil, whatever.... of course it was. Duncan apologized as he stabbed him, but Duncan felt (and was correct in) believing that it was necessary. That doesn't make it "right" but that also doesn't make it any less necessary.
If to stop a Blight Duncan needed to bathe in the blood of a hundred virgins and eat a newborn baby, then that's exactly what he'd do. He'd slaughter each of those virgins himself, and roast the baby over a spit while taking his bath. He'd also feel no remorse in doing so, because in his mind he'd see: a hundred and one lives in exchange for the lives of every other person in the world. That's a small price to pay.