It seems that the coordinate system MD2's are drawn in is different than the OGL one. My models always point down/up the z axis.. Am I correct?

OGL doesn't make any assertion about which direction is "up"...

And yes, MD2's vertical axis is Z.

Thanks OSC

Would switching the y and z value simply work?

for each axis swap you need to negate one axis, otherwise you get everything mirrored (with opposite winding direction).

When I negate one of the axis, the model starts swaying from left ro right... :/

Edit - I fixed it.. Doing the negation when I interpolated the frames fixed it..