how to unprotect the script tag in the Editor window?

Hi folks,

I'm in need of some serious help. I have a custom plugin where I access the html DOM components to do certain operations.
When ever I include script tags in the source edit window and switch back to the html view, the script tags are being protected.
I found that FCK editor protects the script tag by default while switching from source to html view. I tried tweaking the js files, but i could do it successfully only for firefox, when it comes to IE the editor breaks down the moment i tweak the regex entry in "fckeditorcode_ie.js" file.
Is this the right approach or do u guys have any other way to avoid script tags from being protected??
Please let me know if there is any other way to achieve what i want.
(I need the script tags to be intact in the html view window)

below is the sample code of what it looks in source edit window:

<div id="sample">
<div>
..
..
</div>
<script>
(Some scripts)
</script>
</div>

This is what i get from the html view when it is accessed through code(innerHTML):

<div id="sample">
<div>
..
..
</div>

</div>