To give an update on this. I was able to successfully swap out the PERC 5/e card with a LSI SAS3801E card.
FreeNAS detected the disks with the new SAS card just fine and was able to import the pool as if nothing had changed. I believe this was due to the fact that the RAID-0 volumes stored the RAID metadata at the end of the disk (PERC 5/E follows the DDF standard).
With direct access to the disks I was able to determine one of the disks was failing in SMART tests. I replaced that disk and resilvered the array.
After the resilver the Permanent errors disappeared. I also did a scrub to confirm that everything is clear,
Code:
~# zpool status -v
pool: backup
state: ONLINE
scan: scrub repaired 0 in 61h16m with 0 errors on Wed Sep 24 23:34:34 2014
config:
NAME STATE READ WRITE CKSUM
backup ONLINE 0 0 0
raidz2-0 ONLINE 0 0 0
gptid/83030910-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
gptid/83616d59-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
gptid/83ac6c71-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
gptid/83ff8106-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
gptid/84331ce3-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
gptid/846d5967-d43e-11e2-9993-001e4f206cc6.eli ONLINE 0 0 0
raidz2-1 ONLINE 0 0 0
gptid/320e7bcf-d52f-11e3-8662-002219099607.eli ONLINE 0 0 0
gptid/0566b96c-255f-11e3-bb68-002219099607.eli ONLINE 0 0 0
gptid/ef15bf70-3545-11e4-be52-002219099607.eli ONLINE 0 0 0
gptid/0663f4bd-255f-11e3-bb68-002219099607.eli ONLINE 0 0 0
gptid/06ca9e5f-255f-11e3-bb68-002219099607.eli ONLINE 0 0 0
gptid/0729c039-255f-11e3-bb68-002219099607.eli ONLINE 0 0 0
errors: No known data errors