The gedcom file is only used during the import. The import process creates new records in the WikiTree database tables for all the people who are being added and puts the data that is in the gedcom into all the fields that get displayed on the profile page. Once that is done, WikiTree will never again use the gedcom file for anything, so there is no reason why it has to be saved forever.
That said, I have noticed that WikiTree does not only save gedcoms, but make them available to look at by displaying a link to them in the sources initially and will always have that link as the earliest entry on the change page ... except for this case, that is!
The gedcom import process allows you to delete a gedcom file that you uploaded BEFORE you import it. That's a good thing - if the import request gets approved and you look at the profiles that will be created to decide which to skip, etc. then you can choose to simply delete the gedcom file instead of importing it. Once it has been imported, though, I don't believe there is any way for the person who uploaded it to delete it.