TinyMCE repositioning <span> tags - tinymce

i've seen some TinyMCE editor questions here before, so figured it was kosher.
Using Version 3.1.2
I have a "glossary" I am trying to use and on save, the code is getting repositioned so that portions of the glossary that need to be hidden are not.
It is taking a <UL> and placing it outside of a <span> tag I have.
The following code:
<p class="hide_def">
<span class="term_title">Investigational</span><br>
<span class="def">Definition Here
<ul>
<li>Definition Bullet Point</li>
</ul>
</span>
</p>
Is being changed to the snippet below. This throws all of the <UL> tags outside of the definition area.:
<p class="hide_def">
<span class="term_title">Investigational</span><br>
<span class="def">Definition Here</span></p>
<ul>
<li>Bullet Point</li>
</ul>
I have heard of turning off the "cleaning" config setting in TinyMCE, but also heard that is a bad idea.
What can I do here?

Since tinymce version 3.4 deactivation of the cleanup functionality is not apossible anymore.
With your version you can set the tinymce config param cleanup to false:
cleanup: false,

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