Disable all automatic behaviour

I use CKEditor in my homebrew CMS. I really like it except I've got a problem with the auto-wrapping.

Because I use templating + custom logic to let my clients insert custom content the input in the CKEditor isn't exactly valid HTML. E.g.:

<ul>
    <li>one</li>
    [[if (val==true)]]
    <li>two<li>
    [[endif]]
    <li>three</li>
<ul>

However when I save this HTML source my CKeditor automatically wraps my logic in in li-tags like this:

<ul>
    <li>one</li>
    <li>[[if (val==true)]]</li>
    <li>two<li>
    <li>[[endif]]</li>
    <li>three</li>
<ul>

I managed to disable this behaviour for p-tags and div tags, but till now I've been unable to disable it as a whole or for lists in this matter. Can someone push me in a direction to hack this functionality out of my CKEditor? Would be awesome!!

Kind regards,

Daniël