The short answer to the AMM barrage is "More PD Ships"
in Aurora, Missiles barrages tend to be either overwhelming or completely ineffectual. Since they run out, and can be completely neutralized, always bring enough PD to neutralize them.
My strategy in my no-missile games is 50% by tonnage dedicated PD ships in my fleet. If the enemy is bringing missiles to the fight, I'm happy. It means that I only need a few beam ships to mop up after they waste their barrages. With the change to still be able to shoot down missiles which can cross the distance in less than 5s, and the change to fix missile tracking bonuses I can choose to either wait at max range to give my PD the best chance to hit (if they're using more than I think I can handle) or close in and kill them before they use them all (if I know I can take the salvos).
If they are beam heavy and I didn't tailor my fleet due to proper scouting (like a first encounter with an NPR) then I will either need to retreat, or take advantage of point blank gauss spam, which is highly effective, so long as my ships are faster than theirs.