Permission to Reply to Comments
Edit your comments.tpl.php file and delete the &lt;?php print render($content['links']) ?&gt; 

Then all you gotta do is create your own reply, edit, and delete links


reply is /comment/reply/[nid]/[cid]
edit is /comment/[cid]/edit
delete is /comment/[cid]/delete


So use PHP to load the nid and cid and replace the [tokens] with your PHP code. 

Then use PHP if statement to check whether login (global) user is of role x, if true, you print the reply link.

For edit and delete links, you check if login (global) user uid is the same as comment author uid.