Bear in mind that I'm not in the alpha phase, but maybe the solution is simply to reduce the accuracy of the gimbaled weapons slightly? That way you can still target the subsystems, but you just don't hit them quite as often. At least for the subsystems on the smaller ships.
General Dodonna: "...The target area is only two meters wide. It's a small thermal exhaust port, right below the main port. The shaft leads directly to the reactor system. A precise hit will start a chain reaction which should destroy the station... Only a precise hit will set up a chain reaction. The shaft is ray-shielded, so you'll have to use proton torpedoes."
Wedge Antilles: "That's impossible, even for a computer!"
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