Your main weapon will be long-range secondaries. There have been a few coders who made guns that track your target, but this isn't necessary. All you have to do is give the player long-range, fast heatseekers that act like a target-tracking gun.
Basically, you'll have to create new weapons to compensate; maybe a high-damage, high-rate-of-fire primary would do the same job.
it moves so freaking fast no matter how low I put it's accel.
The acceleration value is counterintuitive; the lower the value, the higher the acceleration. So lowering the value isn't going to make your ships accelerate slower. Try raising it.
For example, as your speed gets higher, the acceleration in the same (general) direction you're heading gets lower and tends to 0 as it aproaches some kind of top speed. In theory it would make the fighters have a top speed but it harder to notice when compared to the original FreeSpace.
Perhaps a slow-recharge afterburner; once the burner is worn out, your acceleration is much slower. Just a thought. I think that the target will have enough time to accelerate to high speed regardless.
I'm interested in any kind of newtonian development in FreeSpace; it always bugs me how ships travel slower than bottle rockets.