Seeing how they made Fallout 3, Sadly, I doubt they ever will. RPG games isn't what Bethesda is good at. It requires good writing and imagination. Two things their fans don't seem to care about.
It's not really, "RPG games isn't what Bethesda is good at." It's, "Fallout isn't what Bethesda is good at." The Elder Scrolls is their home ground and they're good at doing those. But when it came to Fallout, they just dropped the ball on morality and story. I just felt like too much was pushing you towards being like dear old dad. So I agree with you, on a Fallout RPG.
I doubt that Bethesda will leave the option open in a future Fallout to go through the game without killing.