There is almost certainly an mccli command that will do what you need. How are you disabling these clients through the GUI?

Under policy tab > clients> Select client name and then edit> tick the checkbox for disable all backups.

I apologize for the delay in getting back to you, I've been having some issues with my lab environment. The following mccli command should do what you need:

mccli client edit --domain=/path/to/client --name=clientname --enabled=false