Prevent admin/Jamf Pro from accessing/deleting 2nd partition
Having 2 different "OSes" on 2 partitions should allow you to encrypt them indivually. 

If you create a new partition, install mac there, and enable Filevault there, it should not be readible from the other boot partition. 

I don't think you can stop it from being deleted though. If the software has admin access it can do what it wants with the disk.