No way in hell FIFA bans Uruguay from the World Cup. If it does, then CONMEBOL must withdrew to play in solidarity to Uruguay, and if Conmebol even hints at something like that there's even less way in hell of it happening...
Something similar happened with Chile in 2009, before the 2010 world cup. Rangers, a 1st division team, was relegated after being penalized with three points for fielding an extra foreign player. They then took the case to court, and then FIFA stepped in and warned that Chile could miss out on a World Cup spot. Obviously, Rangers took down the case and nothing major happened afterwards. This is a much more obvious case of government intervention, and even then FIFA didn't really make a big deal about it. Another case happened in late 2008. Peru was banned from all international competitions, even club level, after their Insititute of Sports (a government body) didn't recognize the FA's elected president, if I'm not mistaken. About 3 or 4 weeks later, FIFA and the Peruvian FA came to an agreement and everything was resolved and in 2009 everything went on as usual. This was the harshest punishment I can remember FIFA giving for government intervention, and given that it was solved pretty easily, and that Uruguay's case is very different and much farther from being government intervention, I don't think FIFA will even begin to worry about banning Uruguay from this World Cup or future ones.