If I'm understanding you correctly, you could try modifying tpl_index_categories.php
At about line 67 there's the line:
if (PRODUCT_LIST_CATEGORY_ROW_STATUS == 0) {
// do nothing
} else {
// display subcategories
/**
* require the code to display the sub-categories-grid, if any exist
*/
require($template->get_template_dir('tpl_modules_category_row.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_category_row.php');
}
?>
You could try changing the first bit of that to check for this being the home page:
if ((PRODUCT_LIST_CATEGORY_ROW_STATUS == 0) || ($this_is_home_page) {
// do nothing
} else {
........
Don't have time to try it out, but worth a shot -- I'm not 100% sure if the variable $this_is_home_page is in scope at this point. Usual disclaimers apply, and you should obviously backup any file before modifying them

Paul