City have got into Europe because Manchester United, Chelsea, Arsenal, etc can play fair, not because they can play fair themselves. Whichever country came 2nd to the prem in the fair play league should've got the position IF the team that topped the fair play table hadnt qualified. Basically all the national winners of the fair play league should be taken, and the best one who hasnt qualified should get the spot, not find the fairest league (bear in mind fair play takes in some utter tosh reasoning such as 'spirit of the game', what a fair judging characteristic) then give it some team that came 6th.
End of the day, City played fair against the teams below them, because they dominated play and didnt need to foul. When up against it, they fouled, hence why they didnt come top. Sad there being rewarded for it really.