Is there a way to completely remove or deactivate the external TOC? Would the code be written in the NCX file or elsewhere? If code could be provided that would be helpful as well.
You cannot deactivate/remove the ncx file. As the epub will not validate without it. Why dont you just simply remove all the links from within it, that way, if a reader does open it up in a sidebar it will simply show a blank screen. Not really user friendly though. I would recommend you add atleast one entry, pointing to the start of your book or your "internal toc". Taking the above into consideration your navmap inside your ncx file would look something like this:
<navMap> <navPoint id="navpoint1" playOrder="1"> <navLabel> <text>Your book title</text> </navLabel> <content src="page1.xhtml" /> </navPoint> </navMap>
@Morne's answer is correct; you cannot totally disable the NCX file but of course you don't have to put anything (or very much) in it.
However, another option might be to build an ePub 3 file - the NCX is optional in ePub 3, so you could just omit it. That said, I do not know how existing readers render ePubs which do not contain an NCX.