To properly handle slaves and logic and stuff, it would probably be best to change the logic system, so that you can "deactivate" any number of slaved slave blocks or weapon blocks. Imagine hitting a single button, and it deactivates a logic block that has half the weapon blocks, half the slave blocks, and half the effects blocks slaved to it. You would be able to instantly halve the weapon power at the push of a button (or logic!).
Similarly, you could slave only the effect or secondary weapon blocks to the activation block, and change the effect (and to a lesser extent, the power usage and damage potential of the weapon). Example: Push a button to make your weapons fire at half-speed, more damage per shot, or rapid-fire and less damage per shot, simply by slaving half the secondary cannon blocks to an activation button. (Instantly changing an example c/c weapon system with 100/100 cannon/cannon construction to 100/50 cannon/cannon for slow-fire, heavy-hitting bullets, or something like that.)
Similarly, if systems were to obtain any kind of slave-block system, using this logical block control would translate directly to that, allowing the pilot incredibly detailed control of their systems, all depending on how skilled the ship builder is at logic constructs.
Best of all, this modified idea would fall neatly into the devs' plan to have block control on everything, instead of relying on more conventional input methods. (Read: slider bars and numeric data entry.)