You're correct that it's not necessarily moral. However, having an actual, enforceable system in place does mean that at the very least there's some kind of rhyme or reason to what happens. As it stands there's nothing stopping anyone from doing whatever the hell they want and the UN effectively can't do a thing, even if it's against the geopolitical rules we (countries) all, ostensibly, agree to. When any non-justification gets through without so much as a sanction or a dirty look, the system is -- well, it's not even broken. It's just non-existent, and I'd rather live in a world where some law was preventing any country from doing anything at any time.
You are philosophically correct, I want to stress that - I don't think that giving any organization the ability to decide what is and isn't allowed wholesale is inherently good. But I think it's better than letting world power governments get away with literal murder because of their power. I would consider that an outright failure of the organization to "protect individual human beings, not to protect those who abuse them."