Deletion is not a preservation mechanic. It is a removal mechanic that we preserve for review but it is not in itself a means to preserve things in their last state. It is in fact a means for cleanup, and in that mind, allowing comment deletion is also helpful towards that goal.
We allow authors to delete their own comments in case they made mistakes, or they are alerted of the comment no longer being necessary, and a host of other very reasonable things. None of these particularly cease to apply once an answer has been deleted. Certainly, there's the potential for an author to delete a useful comment, but there's no reason that being on a deleted post, wherein to the majority of users the comment is already gone, it should be protected from deletion.