It was established years ago, that WoW is non-canon. So that's a non-issue, luckily.
The trouble with re-making WC1 and WC2 is that narrative back then was hardly more than short flavor texts (at least from my rather short experience with the first couple of missions in WC2 it seems that way). I don't know how fleshed out the story is in additional novels and the like, but I imagine that bringing it up to speed with the narrative and presentation quality of WC3 or SC2 would take some serious effort. The gameplay needs to be re-worked - much of it is not up to current RTS standards: mission design, unit variety, pace, etc etc. I doubt that it's much less work than creating a completely new title. And I think a WC4 would be better received. At first I was a bit undecided whether there's more people who'll say "Hey, I'm playing WoW and I always wanted to know how this whole thing started" or if there are more who are like "Meh, I already played that or heard most of the story.", but I don't think the majority of WoW players care all that much about the story but about the game itself.
Plus, I think the last thing Blizzard needs after getting so much flak for SC2 and D3 not being innovative, is to remake their old games.