How to configure ipv6 on Mac OS X to ping its own address?

Those packets are either blocked or corrupted by a network appliance or OS X itself (pfctl).

If you are certain that Stealth Mode is disabled I would launch a packet capture with Wireshark and see if you get anything back from your ping6.

If you have an other computer I would try to ping6 :

Mac WiFi <=> router <=> PC Ethernet

Mac WiFi <=> router <=> PC WiFi

PC WiFi <=> router <=> Mac WiFi

PC WiFi <=> router <=> Mac Ethernet

Mac Ethernet <=> router <=> PC Ethernet

It would help you to figure is Mac is not able to craft/receive ping6 packets over WiFi, or if the issue is located to the router. You can also check the router firewall logs to see wether the firewall block those probes.