Clauses are void but that doesn't mean he will play. I think Atletico are thinking long term as by the sounds of it future transfer dealings could rest on it. The two clubs have a pretty good relationship too so there is the obvious worry of ruining that too. I think he'll play but just because Uefa have said he can it doesn't necessarily mean he will.
I remember Mourinho saying that both of Pep Guardiolas CL successes where tainted, and that he would not want to win the competition in a similar way. So if Courtois doesn't play and Chelsea go on to win the CL, will that not make there victory tainted too?
It would be interesting to see what would happen if you failed FFP by an amount less than the fee in stipulated in the contract. Personally I'm of the opinion that if AM signed the contract it means they accept the terms of the contract and should cough up or Courtois not play, and UEFA do one. But I'm guessing Chelsea want to keep Courtois and I don't think he'd forget you blocking his chance to play in a CL SF when his contract came up for renewal.