What about AMM ships - do you want some control over which ones fire?
Well AMM ships could indeed be different. Still... the only reason not to shoot in this instance is the desire to conserve AMM.
But would a normal military actually do that? "Let these missiles hit us, in the meanwhile we're conserving AMM". Is that realistic? I understand how a minmaxing PLAYER might do something like this. Because a player is detached and sees numbers on a screen, and because damage in Aurora is by nature too "fixed", and thus predictable. You can predict that these missiles will not take down your ships... But I believe a real military would not take the chance, and prefer to hit the incoming missiles.
The only situation I can envision in which I might want to choose who will shoot is when there's overkill: I have 250 AMM ships, and there's 3 incoming missiles. Obviously in this case, I don't want 250 ships to shoot at 3 missiles... Likewise, I probably don't want to shoot 10 times at the same incoming volley, if I have a technological advantage that allows for that.
An on/off switch might make sense, in this case. Or perhaps, a new fire control operation mode. You could have a "point defence autofire" mode which always shoot at every incoming threat until its down.
A note on what Garfunkel said. Being a third party in a missiles conflict... While I completely understand, I believe it's a rather sticky issue. Because a third party, once missiles are flying, does not actually KNOW whether or not the missiles are going to hit its ships. What if it's all a ruse and both the other contendants are actually targeting your ships? What if the missiles are only pretending to go for the other ships, and are going to change target at the last second and hit your ships? If you are at the location, and there's missiles flying, should you shoot? Would you shoot?
I still think that "beam" weapons assigned to point defence should just shoot down missiles who come too close. If we want to model the "third neutral party" situation better, I think an empire-level switch would be better. You are able to select, maybe in the diplomacy screen, which other races are "friendly" and which are "hostile". Unless you change that classification, friendly ships/missiles are not going to appear in the contact list, nor are going to be targeted by point defence,. If you want to open hostilities, you go to the diplomacy screen, set a race as "hostile", and suddenly all the contacts are going to be available, and missiles will be auto-targeted.
An IFF system, so to speak. Ships and missiles of nations considered "friendly" are not valid targets, unless you change their identification.