Just to pick on Swag's comment
FIFA's threat of sanction to ban teams and nations from competiting in International competition is, in economic terms dubbed, a super threat. A threat that has zero credibility.
Suppose that one that Portuguese teams took the case to the civil court - Why on earth should they be deterred from taking the case to the civil court if the club that is being penalized is not you but others, who ironically enough might have conspired against you? The incentive alignment isnt there, and I bet Blatter didnt read Professor Myerson's articles on revelation mechanisms. Well, I tell him to not bother because he doesnt have the intelligence to understand the point.
And FIFA et al cannot overrule the decisions made at Civil Court. Yes, they may have the power in their regulation to take certain measures but then again teams will have strong ground to void such regulation by repealing again.
Moreover, suppose a independent judiciary and big institution makes certain decisions that goes against FIFA wishes, then just for the PR perspectives they cannot ignore these issues, simply because FIFA is not above the law.
There have been three incidences, which I can remember, whereby football federations had to take on the judgement made by the civil court. That is
(1) Bosman Ruling
(2) Italian Abolition of Non-EU rule
(3) Transfer Market Rule in 2001.
I think it is pretty clear Inter cheated their way to Scudetto and I am now incensed in retrospect that our management team didnt take the case to the European Court.