Solution? `ionice`!
Where `nice` is used for CPU scheduling `ionice` is used for io scheduling and together they can tame a massive rsync.
Here's what the final command line looked like (initiated from a backend server):
rsync --timeout=480 -z --compress-level=9 --rsync-path="nice -n19 ionice -c3 rsync" --recursive --delete-during --delete-excluded /local/path $REMOTE_SERVER:/remote/pathThe magic here is in the --rsync-path parameter where we're defining the path on the remote server for rsync. Instead of using just rsync we're setting a nice'd and ionice'd rsync. Finally the -c3 parameter for ionice is stating that the io scheduling should only occur when the disk is considered idle as to avoid any blocking (especially important for the apache processes which are serving from disk!).
See more about ionice and nice.