To be honest FIFA made a mess of the play-offs, which are not a bad idea in themselves, by seeding them. How can you seed teams who all finished second in seeded groups in the first place?
It was wrong to change the rules during the competition but there is nothing intrinsically unfair about seeding the play-offs.
The qualifying groups are seeded, the draw for the finals in S.A will be seeded, it's entirely consistent to apply the same logic to the play-offs.
What was wrong was that they only decided to do it because the likes of France and Portugal looked like they may go out.