Something isn't right. What is taking ages to load? The obj, or the new ma file? The new ma file should take the exact same amount of time to load as the other ma file. (Make sure you delete the history on the objects after you separate them)

Another alternative would be to export your scene as an fbx file, and then reimport that into a new scene. This will keep your groups.

You're free to continue to use that ma file of course, but I would try the fbx export/import first.