The Courier mission while difficult can give you a decent payoff. The key is to CAPTURE the courier, just destroying it only gives a mediocre payoff. It the courier escapes but your marines were in the process of mopping up, ie your marines outnumbered the defenders just stick around in the mission for a bit longer, the ship will still get captured and you will get the full pp.
If it escapes completly, don't bother staying in the mission, there is no payoff for killing the escourt but missing the courier. All in all I agree that mission should be reworked in how it awards pp.
Another thing is that my experience is that this mission is almost the only mission I ever get in enemy hexes which is real annoying.
btw I have tried to duplicate the wierd double weapons prob that I mentioned a few posts up, but have not encoutered it again, hopefully it was just a isolated incident.