It is hard to tell and it depends whether it really does contravene EU law. No one really knows for certain though. You cannot take EU laws too literally. If you did, only allowing six teams to play in Europe from one country would mean that they are contravening free movement of services. The problem is that football clubs and the football market in general is so different to any other type of business market. In few other markets do you have a Europe wide organisation like UEFA who have such a control over the teams. Also the exact product of football teams is difficult to determine.
On the one hand, UEFA have been speaking to the European Commission throughout, so would feel confident that they are in the right. Also, the rules are not blatently anti-competitive as they could impact upon any team.
On the other hand, and although not directly relevant, the ECJ has very often tended to strike down rules which, in fact, have a negative impact on competition/importers.
To be honest though, considering the extent to which the EU has endorsed FFP and continuously stated the extent to which FFP progresses EU aims too (
http://ec.europa.eu/competition/sectors/sports/joint_statement_en.pdf), I am inclined to think that whilst it will be argued and there is the chance that the court will overturn it, it is most likely that the EU will uphold FFP.
I still think it will come down to proportionality of the fines.
Dupont, as far as I'm aware, is challenging the whole idea of FFP. These punishments are a key part of it and will be used to show that FFP is not proportional to they aims. So, if he wins and FFP is deemed illegal, then it will have an impact on City, etc.