The same happened to me, this is what I did.
I don't know if it's the best way to do it but it works.
Here's the code in your fiddle:
http://jsfiddle.net/ZGsPm/1/
You add extra list items where your ignored sections go and add them a class ("ignore" in the example) and an id.
<body data-spy="scroll" data-target=".main-nav">
<nav class="main-nav">
<ul class="nav">
<li class="ignore"><a href="#no-spy-first"></a></li>
<li><a href="#first">First</a></li>
<li><a href="#second">Second</a></li>
<li><a href="#third">Third</a></li>
<li><a href="#fourth">Fourth</a></li>
<li><a href="#fifth">Fifth</a></li>
<li class="ignore"><a href="#no-spy-second"></a></li>
</ul>
</nav>
Then you add the corresponding id to those sections so you can reference them from the list item.
<section class="no-spy" id="no-spy-first">
Don't spy me!
</section>
<section class="block" id="first">
First
</section>
...
<section class="no-spy last" id="no-spy-second">
Don't spy me!
</section>
And finally, in Javascript (after you called the scrollspy function):
$('.ignore').css({'visibility':'hidden', 'width':'0%'});
Hope this helps!