The only way to get rid of a file once it is written is to delete it. However, the cell itself can be deleted using the command "cellname delete <cellname>", as long as the cell is no longer instantiated anywhere in the design.
I am aware of the problem of leftover unused files from modifying the contents of parameterized cells. As a temporary workaround, I added the script
that will scan a directory for .mag files and remove all the parameterized cells that are not used by any other file. However, I do intend to handle this better in the future, when I get around to working on it.