Actually, Lincoln's own page for CGI.pm lists information on countering possible DoS attacks via CGI.pm, including file uploads:
Another possible attack is for the remote user to force CGI.pm to accept a huge file upload. CGI.pm will accept the upload and store it in a temporary directory even if your script doesn't expect to receive an uploaded file. CGI.pm will delete the file automatically when it terminates, but in the meantime the remote user may have filled up the server's disk space, causing problems for other programs.
Tony