Buying exclusive rights to teams / leagues to cripple the competition is a fairly standard EA play. However it is important to note the exclusive contracts are between EA Sports and the teams / leagues, not FIFA.
The main things FIFA brings to the table for EA is the name, and the World Cup competition. EA clearly things they aren't worth as much as FIFA wants for them, hence the current wrangling.
If the deals falls through then "EA Sports FC" (or whatver it ends up being called) will still have all the teams / leagues locked up. So a theoretical FIFA game from someone else would presumably still have the same disadvantages as Pro Evo etc.