Couple of ways to batch update/delete.
From the front end in the user screen you can filter the users you want to delete, tick the check box to select all and then at the bottom of the screen choose action = delete and click go. that approach will probably allow you to bach delete 100 at a time asuming you can easily filter.
The other way would be to import users and remove the users you want to delete from the list all together just leaving the users you want active in the system. On the import user task make sure you have
Remove users if not present in import file ticked. the risk is if you have a bunch of imports going on you will delete the other users from those imports unless you can group them all together into one master import list.