It depends on the mdl files. If they are a bit older, assimp should be able to deal with them. Also milkshape3d is supposed to support mdl, but I donīt know if it will handle all of them and I have no idea if it has a command line option. But if both do not work, I donīt think there is an alternative to an own solution which depending on the features you need to support might not be much work.
