to break to comment section out like the footer would require total restructuring of the html structure of the template (single.php ?)
as far as i can see, at the moment, the loop with the post and the comments is all in the #content div;
to separate the comments, one would need to close all the divs before, and re-open them – like so (don’t use this a copy/paste instruction – this is just brain storming):
</div><!-- .entry-content -->
</div><!-- #post-## -->
<!--the insert code begins-->
</div></div></div></div></div>
<div id="wrapperwrap-2"><div id="wrapper-2" class="hfeed"><div id="main-2"><div id="container-2" class="one-column"><div id="content-2">
<!--the insert code ends-->
<div id="disqus_thread"><div class="clearfix" style="display: block;" id="dsq-content">
obviously, one cannot re-use the css ids, therefore one would need to create new css ids with exact the same styles as the ones in the insert code; the gap is a bit different, therefore it needs some adaptations in the css, and these are only allowed to be active in single posts.
next problem – how is the disqus code inserted?
if this is a plugin, where does it hook its code into?
and so on …
this is going to be a herculean task …