t() function doesn't render HTML
This code should work for you

$link = l($title, $url);
$my_body_content = t('!frequency new comment(s) sent to !link', array('!frequency ' =&gt; $frequency , '!link' =&gt; $link));
$ewrapper-&gt;field_body-&gt;set(array(
    'value' =&gt; $my_body_content 
) );