How can I prevent a user from killing an application's process via the command line?
Kill the user first?
That is, use your Windows user/workgroup authorities settings and don't let the user see the command line.
If you cannot do someone any good: don't do them any harm....
As long as you did this to one of these, the least of my little ones............you did it unto Me.
What profiteth a man if he gains the entire World at the expense of his immortal soul?