set nobackup
または、バックアップ ディレクトリを /tmp などに設定し、時々パージします。
VIM ドキュメントから (:help nobackup)
'backup' 'bk' boolean (default off)
global
{not in Vi}
Make a backup before overwriting a file. Leave it around after the
file has been successfully written. If you do not want to keep the
backup file, but you do want a backup while the file is being
written, reset this option and set the 'writebackup' option (this is
the default). If you do not want a backup file at all reset both
options (use this if your file system is almost full). See the
|backup-table| for more explanations.
When the 'backupskip' pattern matches, a backup is not made anyway.
When 'patchmode' is set, the backup may be renamed to become the
oldest version of a file.
NOTE: This option is reset when 'compatible' is set.