If your BIOS said the disk is bad due to SMART, I'd worry less about doing a scrub and more about getting a SMART report so you can figure out what's tripping errors. Because I'm over cautious with things like this (you do, after all, only have RAID-Z1), I might even unplug all the working drives. I wouldn't want anything touching them while you have no failure recovery. I'd boot from a flash drive containing something that'll report SMART information (like Ultimate Boot CD). I would not be back into FreeNAS until I resolved my SMART situation to my satisfaction. Scrub finds a lot, but it isn't the be all end all.