Just because part of the problem was resolved doesn't mean all the corruption will be gone. Corruption exists in government and all major sports leagues. For all we know the matches could be fixed. Basically, corruption will exist no matter what we do to fight it. FIFA may have been exposed partially but there's probably more going on.
Things are so entrenched and have been so flagrant that it's beyond the bounds of belief that it could be entirely reversed. Human nature is what it is, and we are talking about huge amounts of money in play - when do we ever see a true absence of corruption in such circumstances?
I believe fifa will remain corrupt after the scandal even if "reforms" happen. I'll believe that fifa will continue buying votes and stage games at a country's expense and that in the future they'll choose a tyrannical country to host the world cup. In stuff like international organizations getting billions in revenue, it comes to no surprise.