I believe you can do this through the usergroup manager > Usergroup > Can Use Reputation... I think (I don't use it, so I'm not positive). If that doesn't work, then just delete this from the template:
HTML Code:
<if condition="$show['reputationlink']">
<span id="reputationmenu_$post[postid]"><a href="reputation.php?$session[sessionurl]p=$post[postid]" rel="nofollow" id="reputation_$post[postid]"><img class="inlineimg" src="$stylevar[imgdir_button]/reputation.gif" alt="<phrase 1="$post[username]">$vbphrase[add_to_xs_reputation]</phrase>" border="0" /></a></span>
<if condition="$show['popups']"><script type="text/javascript"> vbrep_register("$post[postid]")</script></if>
</if>