rsync with ionice

Try ionice:

ionice -c3 rsync -aSv /from/dir/. /to/dir/.

and ionice will set the scheduling class to:

-c 1 (real time - don't use this one on multi user systems!)
-c 2 (best effort "round robin" with -n 0-7 range to set priority on sets of groups to give preference to some processes)
-c 3 (idle only)

eg:

nice -n19 ionice -c2 -n7 rsync -aSv /from/dir/. /to/dir/.
Combines the priority scheduling to the least favorable (19) with nice as well as the lowest priority of any grouped "best effort" process.

Check your results by watching uptime

watch uptime

From:
Backups and rsync jobs taking all your io ?