But is there anyway FreeNAS continue to work with the damaged drive (i think i'll have to wait a few weeks before getting the new drive)? Can't it "mark" the damaged sectors in order not to use them anymore?
Do i have to make another scrub?
The drive is supposed to mark the sectors bad automatically, I think those are the 'pending' ones that SMART reported. Scrubbing will not help if the disk is failing, it could just make the disk fail faster. I think since you're only using raidz1, I would not risk doing anything until you have a new disk. I have a few of the Samsung drives and the first thing I did before using them was upgrade the firmware and run HD Tune Prol diagnostics on it.
The ahci timeouts are only happening with the one disk? It would seem like if it were FreeBSD related that you would see similar errors on the other disks, but Durkation also has a valid explanation. Hopefully a new disk will solve the problem.