Você está procurando a opção - delay-updates .
De man rsync
:
--delay-updates This option puts the temporary file from each updated file into a holding directory until the end of the transfer, at which time all the files are renamed into place in rapid succession. This attempts to make the updating of the files a little more atomic. [...] See also the "atomic-rsync" perl script in the "support" subdir for an update algorithm that is even more atomic (it uses --link-dest and a parallel hierarchy of files).