It seems to me that it will still be an issue as long as there is at least one person who perceives that the US is in the wrong. And I fail to see any realistic view that would say that everyone will ever agree the US acts correctly, rergardless of US actions or policies- SOMEONE will always be upset.

One person alone cannot do what you are saying the missile defense system will protect us from. If one person, or even a very small group of people want to deliver a nuclear weapon, they will not use a missile to do it. They will use some other means. And the missile defense system cannot protect us from that.