The problem is that if you make it so you don't lose points when you lose connection people can simply pull out their ethernet cable/switch off their wireless and be able to end the game without losing points. There is no way to tell when a connection is genuinely lost and when someone decides to pull the plug themselves.
The system here is pretty decent, the fact that you have the opportunity to reconnect (not sure if this applies to all games but it does apply to billiards now and curling/darts). Of course in an ideal world there would never be any disconnections but that's technology for you :)
I can't really see what else FOD can do, apart from upgrade the efficiency of their servers of course, but this assumes it's a problem their end and not yours ;)