But Blizzard says, as they always do: don't worry. The latest word is that 3.0.2 is heading to the PTRs, and it's pretty clear that if 3.0 is going to break everything in the game, that's where Blizzard will find out. Don't forget that we've got months until the expansion comes out (and likely even a few months until the actual patch hits the live realms), which means there's tons of time to tweak and twist and get all of the new changes working with the old content.
This doesn't mean that things won't be broken -- we're curious to see, especially in even older instances like AQ and Molten Core, what things are like with all of the 3.0 updates. But it does mean that they'll likely be broken on the PTR -- in a few months from now, when this patch finally goes live, Blizzard should have most of the wrinkles evened out.