Director Jon Chu did a question and answer session after the screening of G.I. Joe: Retaliation that I went to He was asked if Duke was really dead, and he proceeded to explain how in the G.I. Joe universe you never know if someone is "really" dead, hinting that Duke could possibly return.
I'll just say that G.I. Joe isn't really G.I. Joe without Duke. They did try to kill him once in the animated movie when Serpentor threw a cobra snake into his heart. Of course he survived in the end. While talking to MTV, Chu said something very similar to what he told us when he was asked about Duke coming back,
"You never know, Storm Shadow died in the first one and came back in the second one, and then other characters have died and never come back. The G.I. Joe world, the best thing about it is you never know who's coming back and who's not."
Basically, what he's saying is that if they can get Channing Tatum back for a third film, then yes Duke will be back! If not, then he will just stay dead. I just think they need to scrap the current trajectory that this franchise is on and start over.
Chu is currently writing the third film with Evan Daugherty (Snow White and the Huntsman and Ninja Turtles). I'm not holding my breath for this third film. I'm sure it will have a couple cool action sequences but other than that it will be an empty film, just like the first two.