Using Rsync For Exact Copy
Rsync isn't the best choice for Mac to Mac copies.

I'd use ditto or asr if you need a command line solution. Disk Utility calls asr internally and you could mirror the volume and then wipe and run Migration Assistant - that's far better than trying to boot from a damaged copy.

Do go ahead and make the full copy for your backup - then consider installing to a new OS.

In fact, you could install OS onto an external USB / Thunderbolt / FireWire drive first before even making a copy then migrate the data and accounts and apps from the internal drive to the external clean OS install.

That saves a step and you don't even need to worry about syntax of asr or ditto or rsync