Some of this discussion reminds me of FreeSpace 2. In that game, the size difference between the fighters and capital ships felt immense. You were rarely targeted directly by the big guys and occasionally, rarely, you would get get in the anti-capital ship beams and get obliterated instantly and hilariously. Even if you had spent god knows how long in the battle and now had to redo it all, it was such a hilarious way to die you didn't much care.
I don't think the big guns should magically miss fighters, that sounds awful and frustrating. But maybe there can be gameplay tweaks made that make it unlikely or impractical for you to want to use the big guns against fighters and hell, if you do, why *shouldn't* they die?
Fleet composition is also an important factor. The missions we have today are typically very large force on force battles but, correct me if I'm wrong Alex but battles in the campaign won't typically be that large. Fleet composition will be important and we may not be able to guarantee that we have sufficient anti-fighter capabilities at all times. Hell, I've certainly lost my fair share of missions when my Apogee got caught without any fighter support and was shredded by those filthy low tech fighters!
Btw, having played a lot of Skyrim lately, I dig the concept of perks. Is StarFarer going to have something like that when you level your captain? Buying perks that improve the speed of torpedos/bombs shot by your bombers or that give your fighters procs that allow them to occasionally dodge capital large munitions or get speed boosts temporarily after killing an opponent could add a lot of flavor.