Apparently Blizzard have released a patch today that supports IPv6.
They seem to have been sensible with an IPv6 controllable option which is greyed out if you have no IPv6, unticked by default if using toredo or 6to4, and ticked by default if you have real IPv6.
The patch notes confirm this. I'll be testing later when I get home.
But cool - at least someone is on the ball now - well done Blizzard.