Thanks Lou.
Ok, so assuming it was that simple, assigning all other players with 0 points for that game - would that affect the statistics?
For example, (technical stuff) - the profile score views etc would take into account all those games of 0 points and it would look like those players actually participated in the games (they would appear in the Games view with a score of 0.
I am trying to think of ways around this , lets take a step back-
Ok, so I re-read your post - basically, the average is exactly that, the average (points won over games played). Hence currently I think it is 100% correct.
Perhaps this is just a UI issue then - you want a quick way of adding players to a game with a score of 0 (they did not really play the game, and did not win 0 points, BUT you want to say they played x (4 in this example) games.
So... there could be 3 ways around this (I need to sleep on this and think on it more):
1) A new scoring method which does NOT average over num games, it averages over the maximum amount of games a player has played in a league and would be the same for all users (essentially giving the /4 average but without having to record them as played 4). So those playes would still have
"Games Played = 3" but their average would be Points Won / Num Games in Season
2) A UI change that adds all the other players to the current game with a score of 0 (I could be more inventive here - perhaps an "Add All League Players" button is needed anyway if all your members play each game anyway - easier than selecting each time. I could then add a Default Points value for a Season (so this would be 0) and they would all be added as 0 and you update the people who did actually play. So this adds a bit of value and flexibility and would solve the issue (even though those players would show up as playing when techincally they didn't (this is what is bugging me 
3) Would the "Top X Games" for a season work? So you have a "Score the top x games" at Season level and the league would use this value for your average. I am not sure if this would work in this example:
Score Top 5. Player 1 has played 6 and Player 2 has played 3. It's the same issues again, unless it divided by 5 for both of them...
It's very late here so hopefully I'll dream about the solution - let me know your thoughts 