Well if this isn't dead yet, I might as well chime in, as I of course had the brilliant idea of doing a 40k mod today at work. Might have some gameplay/lore insight that could help the transition into Starsector.
Turrets and 'actual' weapons are pretty well separated in BFG. Fortunately there aren't a ton of different weapon classes, so moving everything 'up' a step could help keep the ships weapon loadouts accurate: Small weapons would only be for point defense turrets (heavy bolter or lascannon batteries, what-have-you), while Medium would be for Frigates and Destroyers, along with dorsal batteries on cruisers. Large would be your typical cruiser broadsides. Anything else is pretty ship-specific and could just be a built in weapon, like say a Nova Cannon. For missles you really only need to beef up the annihilator rocket launcher to be suitably dangerous and stick to small missle mounts. Torpedoes are a pretty universal weapon and act pretty much just like that on the table top- they even always divide into twos. So one launcher for a Cobra, four for a Lunar - done.
I also wish there was a way to enforce race-specific weapon restrictions. The thought of a Lunar cruiser with an Eldar Pulsar Lance and Railgun batteries makes me squirm. Making all Imperial/Chaos/Space Marine hardpoints purely ballistic and all Eldar hardpoints Energy could solve the problem if you made a seperate set of weapons for each type of mount, I suppose. Then orks could have all universal slots to encourage their looting ways. Sort of falls apart when you start adding the later race additions, though. Especially Tyranids, would hate to even be able to equip one of their guns on my pristine Imperial cruiser.
Other than that, ship defenses are the only other thing I really thought of. The 'phase cloak' in Starsector is already a pretty good approximation for an Eldar holo-field (aiming right for them and still missing), so no real work to do there. And I guess all ships would have 360 degree front shields, but no real harm either way I suppose.
If you need any lore help or information gathering about ship weapons or classes, or naming let me know. I have a pretty decent library of the Rogue Trader RPG, which would be a great source of additional information. The space combat in that actually ended up borrowing pretty heavily from BFG, and it has more specific information on different ships including non-combat vessels.