For Code Behind:
Way 1 : Remove the server code from source and keep the anchor tag in a panel or div with runat="server" attribute. So you can set the visible property from code behind after checking appropriate condition.
Way 2 : Rather than using anchor tag. Substitute it with hyperlink control. It will render the same anchor tag with the server side control over it. So you can hide show it from code behind using its visible property after checking appropriate condition.
And if it is necessary to do with Source only than replace it with following
<%#if (Convert.ToInt32(Eval("article_comment_counter")) > 0)
{%><a href="articles_comments.aspx?article_id=<%# Eval("article_id")%>"><%# Eval("article_comment_counter")%>comments</a> | <%}
else
{%><i>0 comments</i>
Hope it helps :)