Answer (just to share some hours of experience):
To get rsync and sql-sync to work on remote server using Windows (w/Aquia) it is necessary to make changes to 2 files filesystem.inc and SqlBase.php
First delete cygdrive/ from $path = preg_replace('/cygdrive/(\w):/', '/${1}', str_replace('\\', '/', $path));
in line 61 of filesystem.inc
and change drush_shell_exec('gzip -d %s', $input_file)
instead of
drush_shell_exec('gunzip %s', $input_file)
in line 144 of SqlBase.php
Happy Syncing!