You're definitely not the only one to want manual ship control with mouse/WASD. I'm planning for this to be a mod you can enable once I have modding support working.
This isn't exactly what you're talking about, but the next release (coming within a few days, I think) will give you more control over individual weapons, letting you give them individual targets, turn them off (allowing their crew to go do other things), or hold fire unless given a specific target.