Reorient joints

Simply rotate the bone (might be best to do this in the bind pose frame) to the orientation you want & hit the Align Capture Pose button in the Rigging shelf. Remember to clean the rotations out of the joint and adjust the child-bones too (maybe there is a way to fix a joint without affecting it's children? un parent first maybe)

Update - the bracketed suggestion works.. remember to turn on the Keep Position When Parenting when you detach though...