While it's certainly not a direct replacement, I think the two are close enough that Canon is unlikely to update the 100-400mm any time soon.
Unfortunately, I agree. A new 100-400 zoom, even if it is $500 more than the current model would probably undercut sales of the 70-300mm and unless a third party produces a quality competitor (are you listening Tokina!) Canon is under no pressure to upgrade the lens. The reviews I've read of the Sigma 400mm zoom are not too promising and the "Bigma" apparently has some serious autofocus issues.
I'm not sold on the idea that a 70-300 is anything at all like a 100-400... they're about as similar as the 70-300 is with canon's 70-200 lineup, maybe less so. 70-300 is a generalist telephoto range, 100-400 really screams dedicated sports/wildlife lens; the 100mm makes a huge difference.
canon could also choose not to directly update their 100-400 and go with a variation:
200-400mm fixed or variable aperture lens (I would love that)
100-400mm fixed aperture lens (I'd swing for that one as well)
all of these would have some value-add which would further help canon justify increasing the price tag on the lens