You need to look at the htmlawed plugin, it filters input.  There are hooks you can use to change some functionality without outright disabling it.

@Matt - Do you know which particular file to edit in HTMLawed.... and whihc particular hook do you mean

for example, this was the code i editted in tnymce
<!-- include tinymce -->
mod/tinymce/tinymce/jscripts/tiny_mce/tiny_mce.js">
<!-- intialise tinymce, you can find other configurations here http://wiki.moxiecode.com/examples/tinymce/installation_example_01.php -->

tinyMCE.init({
mode : "textareas",
theme : "advanced",
theme_advanced_buttons1 : "bold,italic,underline,separator,strikethrough,justifyleft,justifycenter,justifyright, justifyfull,bullist,numlist,undo,redo,link,unlink,image,blockquote,code",
theme_advanced_buttons2 : "",
theme_advanced_buttons3 : "",
theme_advanced_toolbar_location : "top",
theme_advanced_toolbar_align : "left",
theme_advanced_statusbar_location : "bottom",
theme_advanced_resizing : true,
extended_valid_elements : "a[name|href|target|title|onclick],iframe[height|width|src],img[class|src|border=0|alt|title|hspace|vspace|width|height|align|onmouseover|onmouseout|name],
hr[class|width|size|noshade],font[face|size|color|style],span[class|align|style]"
});

maybe there is more I need to do within that plugin in too...?

The htmlawed plugin passes the Htmlawed library configuration variable through the plugin hook [config, htmlawed]. In your plugin, you would handle that hook and make the necessary changes. No need to alter any core files.

You should also override the js/tinymce view rather than modifying the core. :)