I don't have a D6 site around with revisions enabled so I can't test this, but the following code should disable the custom template for the revision pages:
function MYTHEME_preprocess_node(&$vars) {
$template_name = 'node-content-type-name';
// Work out if we're on a revision page
$on_revision_page = arg(0) == 'node' && is_numeric(arg(1)) && arg(2) == 'revisions';
// See if the rogue template file is available as one of the suggestions.
$template_index = array_search($template_name, $vars['template_files']);
if ($on_revision_page && $template_index !== FALSE) {
// Remove the rogue template file from the suggestions.
unset($vars['template_files'][$template_index]);
}
}