It's still hard to believe how this user was able to remove Super Users permissions - it really takes some efforts to achieve this. Again are you sure this is the case ? Are you getting any special message when trying to login?
It can be just that he disabled some plugins.
I would suggest first to check with PHPmyAdmin in the extensions table to see if the following plugins are enabled :
plg_user_joomla
plg_authentication_joomla
If they are not enabled, their value will be '0', so re-enable these plugins by changing the value to '1' (no quotes).
If this is not the case, and you are sure the issue comes from the core permissions that have been changed in the global configuration, you could try run the following sql query within PHPmyAdmin.
update `jos_assets` set `rules` = '{"core.login.site":{"6":1,"2":1},"core.login.admin":{"6":1,"7":1},"core.login.offline":{"6":1},"core.admin":{"8":1,"10":1},"core.manage":{"7":1},"core.create":{"6":1,"3":1},"core.delete":{"6":1},"core.edit":{"6":1,"4":1},"core.edit.state":{"6":1,"5":1},"core.edit.own":{"6":1,"3":1}}'
where `name` = 'root.1';
This will revert the default core permissions for the core usergroups.
In the case that you have the core usergroups but have custom core permissions, the above code will also change this and after a possible successful login, you will have to re-do your custom permissions.
Note that it won't work if you have changed and created custom usergroups. In this scenario, let us know so we can work it from that point.
In any case, backup your current database before doing anything manually in there.