Hi Cyke,
It is perfectly OK to use both OSPFv2 (for IPv4 NLRI) and OSPFv3 (for IPv6 NLRI) at the same time. However, it is remarkable how different OSPFv3 turned out from OSPFv2, given they share the same name. If it is not too painful to convert to IS-IS, then there is a lot to be said for the extensibility of IS-IS. It would be easier to subsequently add IPv6 to an existing network running IS-IS (as mentioned by the other poster).
Rgds,
Guy