Can I limit the usage of the app to specific agents?
Yes, you can. Zendesk allows setting Role and Group restrictions to control agents' access to apps.
To limit or allow usage of Email Tracking, go to Admin > Apps > Manage > Email Tracking:
Under INSTALLATION, select the restriction(s) you want to set:
You can select multiple roles and groups. If you select multiple roles (and no groups), the agent only needs to be in one of the roles to have access. And if you select multiple groups (and no roles), the agent only needs to be in one of the groups to have access.
When you’re done, click Update to apply the settings.