1. You need to made small modification of your JComments template. Open file /components/com_jcomments/tpl/default/tpl_comment.php and replace:
if ($this->getVar('button-reply') == 1) {
with
if ($this->getVar('button-reply') == 1 && $comment->parent == 0) {
2. At this moment I've no idea how to implement this using template. I'll wrote here if I'll find any solution for this task.