As noted in my answer to your related question there is a datastructre
$wp_filter that stores all information on hooks and filters. You may want to try a
var_dump on it just to see what it looks like. There is no built in variable 'protected'.
This leaves you with two options to keep the administration of the hooks you want to protect: build it into
$wp_filter yourself or keep it separate. I recommend the latter.
Maintain an array
$protected_hooks. I don't know the conditions under which you want hooks to be protected, but you will have to set this array the moment you add an action to a specific hook.
Now, in your tempate file you will need a double condition: is a hook active and is it protected. That would go like this:
if ((has_filter('hook_name') && in_array('hook_name',$protected_hooks)) ...