I'm running IPsec between 3 routers, in a triangle like topology. All traffic from one to the other is IPSEC'ed and i run a EOIP tunnel over that. Including OSPFv2 and v3. And IPv6 will run over that all day long.
Don't know if that will work for you or not. But it does for me.
Thank you. Are you sure your IPv6 traffic is encrypted? If I can't set IPv6 peers and polices I don't see any way to do this but maybe I missed something.