I realize how the scan works in the sense that it has to access the drives which will slow down processes competing for the drive. If the parity check makes the server unusable by design then that is unacceptable, I however do not believe this to be the case or there would be many more posts like this and I would have run into the issue years ago.
Things like Sabnzbd are on the cache drives which don't show much activity during the scan and are capable a lot of i/o yet it still grinds to a halt. This hasn't been an issue until last fall.
I actually have the check scheduled to scan once every two months. However every time it scans it take somewhere around 24 hours or more to complete and as mentioned the server is pretty much useless for that time. The manual scans I have been starting have been for testing purposes.