I would suggest to have users colour the headings using the Shading Color feature instead as this does not copy through when the heading it used in a TOC.

In Word 2003: The Shading colour feature is available on the Tables and Borders toolbar. Apply the shading and then remove the Highlight colour and update the TOC.

In Word 2010: The Shading feature is in the Paragraph group on the Home Ribbon (One with the paint bucket tipping over). Remove the Highlight colour and update the TOC.