Defense from Government Intervention
The scenario you name would be great for cryptocurrencies as it would make them mainstream. As soon as people got sick of govt intervention with Bitcoin in such a scenario, it would probably be relatively easy to get enormous numbers of people to switch over to a very similar (but independent) Altcoin. 

The nature of the cryptocurrency technology is such that it is very difficult to stop people running the software, but a govt could have success in closing down businesses that accept unofficial versions such as the fictional Altcoin. If that happened, it could however still thrive outside of the region being regulated.

Prevention would probably need to occur at a political level, but I'd hope market forces as I've just described will be sufficient prevention as long as no organisation gains too much power over international law. Agreements negotiated in secret like the TPPA are something to watch out for though.