The snakehead was banned by the federal government. ATF, due to their rarity and high price, hasn't become an issue big enough for the feds to notice... yet. With the banning of the snakeheads, something else will become popular and get made illegal at a federal level. What will it be? Who knows.
The reason these fish (and MANY others, at that) are banned in some areas and not others is because the individual States have fish and game departments that evaluate what could potentially become a threat. In my home state of Florida, just about any predator that can survive in it's waters are illegal. This includes my beloved tigers and payara. Now, where I am currently stationed, Missouri, there is no chance that an ATF or payara, or even a piranha, could survive the winter. So, I can have them here.
If ATF get to where every LFS can carry them for $20 similar to the case of snakeheads a while back, they'll doubtlessly end up banned too. I, for one, hope that doesn't happen.
So in short, the decisions are not stupid, but rather well informed and justified.