Best way to completely remove Better Security/Ithemes plugin

Deactivating and deleting it will only remove the plugin files. You’ll have to delete the database if you want to remove all traces of the plugin. You can find the specific database files here: http://wordpress.org/support/topic/how-to-reset-ithemes-security-plugin-to-fix-issues?replies=93

If you do not plan to re-activate this plugin, you can delete the files and you should be fine. Having tables and options in DB should not matter since plugin is no longer there to use it.