Fire Control (Core, p151):
Allows the computer to fire a number of turrets per round equal to the listed number. Alternatively, it can give a positive DM to an attack equal to the listed number, or any combination of the two.
As far as I can see FC software can do PD, but cannot add a DM to a PD reaction.
Virtual Gunner (HG, p64):
Virtual Gunner: A Virtual Gunner package allows a ship’s computer to replace living gunnery crew in an efficient manner. The package can replace any number of gunners, ...
Says nothing about attacks, so shouldn't have any problem doing anything a live gunner can do, including PD.
I'm thinking that the 'best' solution, and the most consistent one, is to not allow Fire Control or Advanced Fire Control to perform PD or affect it, as well as not allowing laser hit-bonus to affect PD rolls. Virtual Gunner on the other hand can
make attack rolls, use PD reactions and take advantage of both FC and AFC (but only when attacking).
Sure, one part of me thinks that if something gives a bonus to hit it should always count, regardless if we're firing on an enemy ship or an incoming missile. On the other hand, the lasers most likely have a separate PD firing mode, where perhaps all the bonuses and computer aids in the world can only go so far, and in the end it's up to the gunner to give it their best shot (sorry, bad pun….).
At first, I did not share your stance on FC, but upon further re-Reading it only speaks of firing turrets, which can be done either offensively or defensively, whereas it specifies can give a positive DM to an attack
and a PD roll is not an attack.
Advanced Fire Control specifies that it's valid for attack rolls only, same as the bonus part of regular FC.