No problem. The users table is just a list, it does not maintain permissions, and deleting users will have no effect.

Security is actually managed through SQL. If you open MMS, instead of connecting to the Database Engine, drop down the server type and change it to Reporting Services and connect to that. Under security, open roles and you'll see the different permission types.

Are these users being disabled in you active directory? Your SSRS site will follow AD credentialing.