Just remembered a dirty way, however you’re doing this on your own risk and by risking a failed update.
Edit your lib/base.php file via FTP/whatever and change:
$tooBig = ($totalUsers > 50);
to
$tooBig = ($totalUsers > 500);
Source: core/lib/base.php at v9.1.2 · owncloud/core · GitHub
However you should do backups as they probably had a very good reason to add this check in there.
And you should really switch to a hoster / package which provides you command line access via SSH.