Из заметки совершенно непонятно в чём смысл этих разногласий.

http://www.fifa.com/en/media/index/0,1369,118144,00.html?articleid=118144
In spite of repeated warnings from both FIFA and UEFA, the commitment expressed by Greek government representatives to amend the law on sport to irrevocably recognise that football matters can only be decided by the HFF and its subordinated football structures has not been respected. In fact, the recently-presented draft of a new law on professional leagues constitutes another example of interference from the government in football affairs. Therefore, the FIFA Emergency Committee has determined that the deadline would not be met by the HFF and that the suspension of this federation was necessary.

Still not clear what is in this draft that is so upsetting,
seemingly more so than the management of sports in Soviet Union.

So, may be times are changing? :)
But you are right if it's some another - and very specific - play between FIFA and Greece apparatchiks :(