Beam Fire Controls assigned to Point Defence ought to choose their targets more intelligently at all. A whole cluster of guns should not be flailing away at a singleton when there are multiple-missile salvos in the same volley. Ideally there would be prioritisation taking into account the capabilities of the defending FCs and the weapons they control (e.g. a slow and short-ranged FC with multiple railguns shoots at the largest salvo because hits scored will be highly variable - it might miss everything, wipe out the whole lot, or anything in between - while a faster FC with a single twin laser turret picks off a salvo that was thinned out but not destroyed). But even if it continues to be a matter of each ship taking their turn, and each FC on that ship firing in turn, not obsessing over the first salvo on the list would allow killing more missiles.
The increased realism option would presumably be to organise what FCs are shooting at what targets then resolve the exchange, rather than resolving each FC in turn before letting the next one use that information to make its decision. It would be nice to be able to have a small number of FC reserved for swatting leakers, but that should probably be a single layer only (i.e. there's the standard intercepts, which might have five FCs firing at each salvo if there's enough of them, then you do the same sort of process to match reserve FCs to leaker salvos, but that's it and you don't get a third try). Perhaps it would also be a good idea to require a high tracking speed for a FC/weapon to be assigned as reserve, representing the necessary split-second reaction time to identify a missile that escaped destruction and then kill it. (Half the missile's speed? Equal? But if it's a decision made by the player setting PD modes the game can't know what will need to be intercepted. So just an additional targeting penalty for guns in reserve mode?)