Though killing a Sectopod is often a team effort... You can abuse it by having the rookie do the killing blow...
Solution would be simple, let any alien remember who gave it how much damage (and what type - as xracer said, taking a Sectopod down with a laser weapon is much easier than, say, with armor piercing weapon) and then after its death distribute the points accordingly.
Similarly these points should be awarded for STUNNING aliens. Given the fact that stunning them is way harder (especially with the stun rod) than killing them, it is quite questionable why the soldiers doing the stunning are not rewarded for it at all.