don't sync the .git directory remotely

This is actually a drush issue - the exclude patterns are generated from the "version_control" engines and there's no such engine for git..

This is in commands/core/rsync.core.inc:

function drush_core_call_rsync($source, $destination, $additional_options = array(), $include_settings_is_default = TRUE, $live_output = TRUE) { files.
  $options = '';
  $vcs_files = drush_version_control_reserved_files();
  foreach ($vcs_files as $file) {
    $options .= ' --exclude="'.$file.'"';

I guess that we would need to create a engine for git but this seems rather overkill for just an exclude pattern.