That's interesting... After playng with the D90 settings the following sequence seems to disable the internal flash.
Under Menu scroll to Custom Settings Menu, select Bracketing/flash. Scroll to 'Flash cntrl for build-in flash' and enter. Select Commander Mode.
Set Built-in-flash Mode to '--', Group A to '--', Group B to '--'.
This seems to completely disable the internal flash. Continues shooting mode works just fine for me.
When the flash is required simply switch back to the TTL mode.
Let me know if that works for you as well or if I am missing something here.