Continuing the discussion from Helpdesk widget, Azure AD guest users and the contacts list:
- Prevent editing of the left navigation (quick launch).
For this purpose, grant a contribute permission level to the non-IT agents. If you need, you can copy it as a custom permission level and set your own preferences.
- Preventing access to HelpDesk settings.
"Settings" are certain pages united by common tab navigation. The pages are stored in "HD" library. Other system files are stored there too (e.g. forms backups, scripts, localisation objects, etc.). You can just stop permission inheritance for that library and remove permissions for non-IT agents (for each separately of for their SharePoint group). In this case the "Settings" link will not be seen by the contributors on the left navigation even without publishing features activated on the site.
- Restoring access to reports.
But when you removed permissions for the "HD" library, the contributors lost also access to the "Reports" pages. To restore it, just grant permissions on folders "Reports" and "Dashboard Designer".