To be honest, I think FIFA will punish the player Byron Castillo, he will pay some fines, be out of a lot of matches, but FIFA will keep Ecuador on World Cup.
If Fifa decides to punish Ecuador, Peru and another teams will probably see a chance to fight to the spot and will be more complicated.
The rules are very clear. If FIFA concludes that Byron Castillo is ineligible to play for Ecuador, then they will be disqualified and prohibited from participating in the world cup. And all their qualifying matches will be awarded to the opposing team by a margin of 0-3. But as I mentioned in one of my previous posts, the chances are low. FIFA has already made the decision, and this time it is an appeal by Chile. Chances of the previous ruling getting overturned are not large, given the previous history of similar incidents.