Sure, this could work, but the user who is deleting a track and its media file may not be aware of the fact that there is a single media file for all the tracks in the iso. Media Center should not be deleting other tracks and the media file in this case, or the user will be very confused of why everything got deleted, and not just one track.
It would be better to ignore "delete media" for an iso, unless you are deleting the last track in the library. As long as there is still at least one track for the iso in the library, the media file should never be deleted. Basically, you implement garbage collection for the iso file. If it cannot be referenced anymore, it gets deleted. But you cannot explicitly delete it.