Norlief,
We've seen both "thoughts" fail spectacularly and without warning. :(
With both scenarios some (but not all) of the problems we've seen are things like:
1. No SMART monitoring, so no way to identify a problematic disk.
2. RAID controllers with their write loophole fubaring the zfs file system without warning.
3. RAID controller "owns" the drives, so ZFS is basically blind to disk replacements and such. (this really shows itself with a disk failure, and pulling a disk from the system with the system running is not the same way to 'test' this)
4. Performance is basically AFU because ZFS schedules reads and writes, and RAID controller reschedule both to try to optimize the pool performance, but that undoes what ZFS has already optimized to the maximum extent.
If you do a RAID6 you are going to have problems as there is zero ZFS redundancy. So if the RAID controller gets hit with a write loophole or other incomplete file system write on a shutdown, your pool might never be mountable (and therefore your data inaccessible) permanently. ZFS will detect the corruption, but if your metadata gets corrupted, kiss the entire pool goodbye. :(
If you do the single-disk array you'll be woefully unaware that your disks have problems. Then one day you wake up and your pool is unmounted because you lost enough redundancy that suddenly the server crashed and rebooted and on bootup the pool is now unmountable. :(
When I did contract work for FreeNAS users I've had many people that paid good money to get their data back after doing some pretty crazy things. The second people use hardware RAID my ability to recover went from pretty good to almost zero. In fact, if someone told me they had hardware RAID I'd tell them flat-out that I wouldn't recommend you pay for my services as the likelihood of seeing your data again was nearly zero, but if you still wanted me to try after recommending against paying me (and I could have definitely used the money!) then I'd give it my best effort. After all, nearly zero odds is better than zero odds. I never got data from a hardware RAID array of any kind... ever. But on non-hardware RAID problems I had about a 90% success rate.
So there is no lesser of two evils. The mechanisms for failure are equally sudden and catastrophic and there is no "safer bet". People keep playing the game of "I have this controller and I damn well am gonna use it, I'm just going to take the safer path with it". So do you want to die by falling in a pit of lava or a rancore pit? Thats basically what you are asking, and the end result is the same. Death.
I'd *STRONGLY* recommend you give up the notion that there is some safer path with the RAID controller. The only safer path is to NOT do what you are doing. If this isn't acceptable I'd highly recommend you go with Windows or Linux (or an OS that actually has the proper RAID drivers, RAID software, etc. to monitor the RAID array) and use a file system that does work decently on hardware RAID. FreeNAS isn't a good fit for everyone, it's not a good fit for all hardware, and its definitely not a good fit for all budgets. So please consider carefully if FreeNAS is for you.
Thanks and good luck with whatever choices you make.