Possibility of Create Site Specific CSS in a Multisite

Question

Yes, you can add website specific class to BODY, for example.

Best approach is to create little multisite enabled plugin, that adds some class to BODY in body_class filter.

function customBodyClass( $classes ) {
  global $current_blog;
  $classes[] = 'website-'.$current_blog->blog_id;
  return $classes;
}
add_filter( 'body_class', 'customBodyClass' );

All themes has to use body_class() function in BODY tag, obviously.