Ugh I had a problem like this too with FBX. Even with the rotate bones command in MED, I was unable to get the whole bound mesh+bones to do it. If and when I did accomplishing something, the whole mesh distorted into this awesome spider thing!

I got around that problem, though, but not using MED to do it. I just rotated the character in my animation application before doing the fbx export, so that she faces the right direction in MED..

Fun fun fun!