Since this is now almost 5 year old thread but still the top Google one it's time for an answer.
Use rsync's --iconv
parameter. It will convert filenames on the fly, from the remote side to the destination.
--iconv=<local>,<remote> for example: --iconv=utf8,latin1
Filenames on the remote side are not affected.
But do realise that you are changing the encoding of the filenames. It might theoretically cause you problems (if they are referenced by other legacy programs/files).