You're exactly right. We definitely have to fudge here to make a game fun. I mean, this far into the future both ship flight and targeting would likely be controlled almost exclusively by computer, but that would definitely make for a boring game.
You could kind of see the issue coming a mile away though. CIG leveled the field a bit by allowing 1x+ hardpoints if you removed the gimbal, but it could have been avoided entirely if gimbals weren't ever introduced on single-seaters.
Since controller parity was a huge goal from the beginning, it seems like an ill-sighted move on their part to introduce a mechanic that can only be used effectively by one form of controller (mouse). Not only that, but to give that form of controller magic auto-flight capability to go along with it.