I agree, missiles need addressed somewhat.
I think a counter project that has a chance to "thwart" an incoming missile/nuke would be a help. Although I hate referencing another world, on (That terrible game that is totally irrelevant and I shouldn't be bringing it up anyways) there's a wonder called an "SDI"
That has a small chance(I forgot the math) to thwart an incoming nuke it's not a huge chance but it's effective. Your opponent then re-launch a nuke if it got shot down until it either hits or he runs out of nukes.
Something like that here would be awesome. You can let your opponent keep firing missiles at you, if one breaks through it does damage and the action points are used up.
However if he/she misses they can re-launch until they either run out or one hits.
Just my 2 cents.