The protection system shifts the threat considerably, because it means the country with it no longer suffers the same threat as the country without it - the concept of mutually assured destruction counts on the destruction of both parties being mutually assured (funny that...), and a protection system means it is no longer mutually assured, one party has a much better chance of coming out with significantly less destruction than the other.
Think of it this way - you and your worst enemy both have guns pointing at each other from a distance of 50 paces. You both know there is enough time to fire back if the other one fires, and you also both know neither of you can move in time to not get hit. If both of you are sane, rational people, do either of you fire? No.
Now consider how that dynamic would change if your enemy put on a full body bullet proof suit of armour. All of a sudden it doesn't matter as much to him whether you fire or not, he is much more likely to survive than before - and he is also much more likely to survive than you are as you dont have his suit of armour.
Gets a little too uncomfortable, doesn't it?