I have a small Ubuntu VM set up with Crashplan Pro (I run everything, including FreeNAS, in ESXi). I made NFS shares, set them to read-only (because I ALSO have the datastores sharing via CIFS and don't want NFS to step on CIFS - this is not "best practice", but it's been working for me for 2 years with no issues), and set up mountpoints in that Ubuntu instance. I'm backing up about 4TB. Same as everyone else, I was looking for a spot to land after the demise of Crashplan Home, but the Pro plan, although more expensive, is still a very good deal, AND they were offering a huge discount, AND they were automatically migrating the datasets over to the Crashplan Pro account if you had a Home account (up to 5TB) so no need to upload all of the stuff again, AND they have encryption on their client. I was using a big random string as my encryption key, and re-entering that key into the Pro client allowed it to pick the backups right up with no issues.
I'm pretty sure you can set up Ubuntu (or your favorite Linux flavor) in a VM inside FreeNAS, or run it on separate PC and it will work fine. I'm also pretty sure it will work if you mount Samba shares the same way and avoid sharing the same files via NFS as well, since this is actually not best-practice.
This has worked perfectly fine with Crashplan Home as well - the Home client never supported backing up shared drives, but running it in Linux and pointing it at mounted shared drives bypassed that limitation beautifully (violating their ToS as well, I'm sure).
I'm perfectly happy with my setup now, and the Pro version officially allows backing up shares, so it's all kosher.