I will assume that you have no SQL servers in your environment which you wish to protect via Backup Exec. If you do (on remote servers not necessarily this server, which I will assume is your designated media server (main Backup Exec Server)) then you should leave it and make sure you have purchased the licence.
From within Backup Exec, go Tools -> Serial Numbers and Installation. Wait for it prepare the installer, then choose local installation, and Additional Options (top option).
Next it will list all the serial numbers it knows about. Is the Agent for SQL listed? If it is highlight and click remove and continue through the installation (no settings will be affected).
If its not listed then let me know, in fact have you upgraded from a previous version perhaps? Or is it a fresh install...
Rob