I don't think asymmetrical bonuses are a good idea. Too subjective.
I think it might be more interesting to remove bonuses for killing fighters of any kind. No landing bonus, but no death points either.
Leave the points only associated with the mission. You need to bomb this much stuff? That's all your points, right there. You get the mission put together in such a way as to accomplish your goals, and you win!
Removes the reward for groups going out and score-whoring all the time (which IMO is a big problem with the FSO). I remember a long time back we had an FSO where I flew with Spit5s across the channel and were bounced by many 190s and 109s. We let some of them go, and they let some of us go. The point was not to kill for score. The point was to get the job done as a team. That's the kind of sentiment that FSO should encourage, IMO. The positive stuff.