Yes, of course. You only need to run it as root OFC. And you probably don't want to backup /sys, /proc and such...
I recommend you mount your mmcblk0p28 to some other directory and then rsync that. Much neater than trying to rsync live root.

Note that to restore that is not so trivial; I'd imagine you cannot rsync back your rootfs when running the said system

I however have found it necessaty to rsync only /home/nemo since everything else can be recovered from images and the apps are easy to re-download from the store.