I don't mind missiles blowing out a gun or two off when your down, but having all your guns blow off is very annoying. The main gripe I have is the explosion area for the missiles in particular to very well knock off all your guns. I say just lessen missile damage area because it's not fun to be 1/4 down in hull and having your guns blown off.
Of course I'm a little biased due to a fight or two against missile spammers.