FIDE respects that every player makes his own decisions and regrets that GM Magnus Carlsen has expressed his desire to withdraw from the upcoming Candidates Matches. It is always a big loss for any event when a player of Magnus Carlsen’s strength is not participating. FIDE’s policy is to review regularly the World Championship cycle after consultation with the top world players. At this point in time, the current cycle is in its final stages and it is not possible for FIDE to change its regulations. In the case of GM Magnus Carlsen not participating, according to regulations GM Alexander Grischuk from Russia will be his replacement.
Have to love the irony in the "too late to make changes" claim, as one of the reasons Carlsen gave for not playing was the fact FIDE kept making changes all the way through the cycle. (Basically, the 2011 cycle was a hot mess. At the time of his withdrawal, no player, Carlsen included, had even seen a contract for the event or reliably knew what the terms would be.)
The championship cycle is shorter, FIDE didn't change the rules in the middle of the cycle. No matches, just a super-tournament to select the challenger. From outward appearances, none of these changes was made in response to Carlsen. (In fact, Carlsen, in his withdrawal letter, states he isn't trying to get them to make changes, just stating the reason he's finding it hard to find the motivation to prepare. Since several of the reasons he gives are still in force today, I'll let others speculate on which of his issues was paramount.)
For trivia buffs:
I think Carlsen in 2011 became the first player in history to withdraw from the same championship cycle twice. He first withdrew from the Grand Prix cycle, which was supposed to select the majority of the challengers, then was reseeded back into the cycle by virtue of his spot at the top of the ratings list (three slots were for the top 3 finishers in the Grand Prix, the loser of the previous WCC match, the winner of the 2009 World Cup, the highest rated player, the loser of the final candidates match from the previous cycle, and one player nominated by the organizers). FIDE's response was to replace Carlsen with Grischuk -- IIRC, Kramnik was the a qualifier from the GP and also the second highest rated so he essentially took Carlsen's spot as the top-rated and his GP qualification went to Grischuk.
If you were looking for punishments, FIDE really cannot force anyone to play in their events, and rarely (I said rarely but I can't think of single instance offhand) punishes a player for declining to play. Chessplayers are not the slaves of any organization, no matter how much some of politicians in charge want them to be.