You can use the remove_post_type_support
for your requirement. In your case, you remove post thumbnail if specific page template is not selected.
function remove_post_thumb(){
if (isset($_GET['post'])) {
$post_id = $_GET['post'];
} else if (isset($_POST['post_ID'])) {
$post_id = $_POST['post_ID'];
} else {
return;
}
$template_file = get_post_meta($post_id, '_wp_page_template', TRUE);
if ($template_file != 'page-your-template.php') {
remove_post_type_support('page', 'thumbnail');
}
}