Go to Utorrent Preferences
In General Select Start Utorrent when system starts and Start Minimised.
Make any Boss Key
Select Use BossKey Password and just make the password whatever you want.
Open Registry
Browse to HKEY_CURRENT_USER->Software->Microsoft->Windows->CurrentVersion->Run
Right Click Utorrent and select Modify
Add "/HIDE" without quotes at the end.
Restart your PC.
Now Utorrent is running but it won't appear in Taskbar, to open Utorrent you need to press the boss key and then password to gain access.
However this method has a loophole that other user can end task the Utorrent process from task manager and start with its executable.
For this you can use Utorrent Portable. Now only you know the location of the executable.