The Monster is Good and Jacob is Evil. Let's just get it out of the way.
The question is: from whose point of view?
The Monster has the most relentless standards. He is, above all, interested in Rules - which makes him Black and White. Both, rather than one or the other. So the clothing in "The Incident" was just another ruse to make us think they would be literal about one being light and the other dark.
Jacob is all about free will. Choice. And that's the gray area. Which means Jacob is - technically - the evil one...but it doesn't make him bad.
The Monster has become twisted by his standards. He might have a noble cause, one we can relate to; but he's still a Monster. That look on his face when he says he wants to go home is more than telling.
So why would a monster need a loophole? What rules would hold him back...except his own?
He needs to find a Loophole through his own Rules. This is why Richard shouts at everyone not to shoot. He knows as long as they stick to the Rules, as long as they don't attack the Monster - essentially an unarmed man as far as they know - they are safe. Richard knows the Rules, which means Jacob knows the Rules.
It's not that the Monster can't kill Jacob - it's that Jacob will never, ever break the Monster's Rules, which prevents the Monster from killing him. So, just as he smashed the roof of the Foot in order to knock Bram out of his ash circle, he convinced Ben it would be a good idea to kill Jacob. He stuck to the letter of the law, which was absolutely fine with him. And that, my friends, is the very definition of Good, as well as of Monster.