Can IPv6 be disabled on an iPad?
No - iOS has no profile or setting to disable IPv6. Even if you jailbreak, I don't know how to set that on iOS operating systems.
Yes I am also using a Hurricane Electric tunnel for IPv6. I have similar problems with my two iMac computers. I have to set my IPv6 to "link local only". This fixed my connection problems.
This partial solution (controlling the router) only works over WiFi though - cellular data carrier routing also would need to be changed if you can't allow IPv6.