System Lockdown on SEP 12

I want to use system lockdown ability of SEP 12 to lockdown unknown machines on the network with a notification to contact a specific team to unlock them. My first testing on this completly locked down the machine and it couldn't even communicate with the SEPM to be unlocked. I had to put the machine into safe mode and uninstall SEP to get it to respond. Is there any documentation as to how to use lockdown while still letting it communicate with the SEPM to get updates/policy to be unlocked remotly?