Im wonder how to configure Config Manager 2007 R2 to allow PXE boot to all machines (Its password protected) without every user getting a message saying they can install windows.
I would consider it acceptable if the users can reinstall windows on their own, but they should not get the ballon message.
SCCM will always display all advertisements for the collection(s) that the machine is assigned to. The only way to avoid this is to not advertise the install until just before you want to image the machine. You could create a new collection which has the advertisement assigned, then add the particular machine to that group when you want to image it.
That's how we do it. We also set PXE boot as the first startup action on all of our machines, and set the OS deployment as a mandatory assignment. That way, we can reimage any machine on our network without ever touching it.