You're going to have to walk all those inodes no matter what you do. rsync is as good as anything at that task.

A better way would be to unmount and send the filesystem with 'dd' or something like that, or, to use 'zfs send' but I have a suspicion that neither of those options are available to you ...

I will say that splitting the rsync job (rsnapshot runs rsync underneath) into multiple, smaller jobs, could save you some time if you're running into any resource limits while you walk that big set of inodes... so if you're lucky and you have 4 or 5 or 8 top level dirs that are all roughly the same size, you could do a handful of smaller jobs, one after the other, instead of one huge one ...