The Server Density tray app runs on login and is used just for configuring the agent and periodically checking for updates.
The agent itself runs as a system service so you can safely disable the tray app from starting on login. You can do this by running msconfig from Start > Run and then disabling the Server Density application from the startup list.
If this doesn't work then you can also remove the "Users" group from the list of permissions on the Server Density agent installation directory so that regular users do not have access. This is usually C:\Program Files (x86)\Boxed Ice\Server Density
Alternatively, an easy automated way to do this on Windows 2012+ 64 bit machines is to run:
reg delete "HKLM\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Run" /v "Server Density" /f
Note that if you do this you will need to manually check for updates. You can also see the latest version from the Servers tab in the Server Density web UI.