The decoupling of currencies from governments sounds like a radical shift, but it's actually only fairly recent in history that we use fiat money. That, of course, allows us to do a lot of things that we've gotten used to in the last century particularly, such as taking advantage of monetary policy to address short-term economic concerns.
If alternative currencies catch on, that's something that governments will have less power to do - or at least, less power to do directly and predictably. Certainly, governments are going to push back on that, and probably try to discredit or disable alternative currencies.
At the end of the day, though, while money can be determined by fiat, value is determined subjectively, so if alternative currencies catch on (which I think they well), it will necessitate a shift in the way that people think about money. (Not unlike the way that the Internet has shifted the way people think about tradable goods and IP law - just take a look at SOPA.)