Generally we have always recommended to not make direct database modifications to our users. The main concern is the possibility of disrupting dependencies and creating orphanated records in the database.

Some modules create references to specific records in profile and user tables. If you manually delete user record but do not cascade this to all the dependent tables you will run in to issues sooner or later.

The more elegant solution would be using DNN API to do this for you. Essentially you need to make a simple custom module that would integrate in to DNN scheduler provider and perform user pruning task for you. There are may be commercial user management modules already capable of this, check out DNN Marketplace http://marketplace.dotnetnuke.com/ for verified 3rd party modules.

You can have sql show you all the dependencies related to the root user table, its just a matter of checking it if you add any new modules / start using new modules in your site. We manually run sql commands to clean up our user accounts, cause we have ran into a similar situation as you. We tried a few 3rd party modules but found some of them do little more then just run deletes on the user table, others work fine and make sure there is no dependencies but they are a bit costly and tricky to verify without buying source / contacting the vendors, it was just easier for us to have sql tell us what the dependencies are and I just check the current listing versus a weekly spot check. Usually before our weekly delete runs.