Small scale or cloud based, sure. Do your stuff without "registering" yourself with any centralized authority. Large scale though, or if what you do has a high level of interaction with the fiat world, it is probably necessary (at least for now) to be a "Bitcoin company" or whatever. 

The way to minimize the risks associated with that is:
1) Minimize exposure to fiat currencies and legacy financial institutions
2) Decentralize your company (register in multiple jurisdictions), allowing yourself to hop to another country in case things go poo-poo in your "main" jurisdiction