I am less worried about beating my chest in superiority as I am in having a sensible system where the whole gamut of force compositions are given a comparable shake in scoring. Ideally, I will never need to think "Hmm, I should really drop this squad to bulk up the other ones" just because I think I will get punished in the soring rather than because I think it will make my platoon better. Likewise, I hope you never need to think "Hmm, I really should break this unit into 2 squads" because of scoring only.
That's easy enough, just compare loss differential based on the point cost of the minis. If the victor has lost about the same as the loser, then it's a minor victory. If there is a greater differential, then it's a major victory. At 1000 points, the math is very simple. If both sides losses are within about 300 points, then it's a minor win. If the victor won by more than 300, it's a major win.
For force destruction missions, the breakdown could be a bit more nuanced: 100 points or less differential would be a draw, 100 to 300 a minor win, 300+ a major win.
That way losing a light mortar, a sniper, and a medic is about the same as losing a full-strength Commando squad, not three-times more as it is using squad count.
UPDATE: I was reading through the rules for the missions last night and came across the section for Attrition scoring. It's very similar to what I outlined above, except they set the boundary at 20% of the point limit rather than 30% (e.g. 200 points for 1000 point games). I think it should work very well for tournaments.