Can you preprocess a specific region in template.php?
Well, you can define your own preprocess function if you want to, since you have all the elements for that. In the theme_preprocess_region function, you can simple do :

$function = 'yourtheme_preprocess_region_'.$variables['region'];
if (function_exists($function)) {
  $function($variables);
}


Then, you just have to define the a function for your region :

function yourtheme_preprocess_region_YOURREGION(&amp;$variables) {

}