Thanks for all the replies! This has been a wonderful source of ideas, and has helped me to flesh out the complications.
As several people pointed out, the big problem is trust. The nanoinfection is actually a much less destructive weapon than the paranoia it generates, which completely undermines many functions of normal society and government.
I guess the problem is that constitutions are based on a very classic view of humans and human relations, and have trouble dealing with things that can change values or modify the meaning of free will ("Free will? Sorry Inga, sometimes it is obvious that you have spent a few centuries frozen. These days almost nobody uses the term because we understand the neuroscience of motivation" - authentic quote from the game). A future constitution would likely need to take such things into account, maybe by declaring what forms of involuntary modifications are allowed and which would make an official unfit for office.
---In game: ----
"Right now" the situation on New America is moving towards the
splintered situation suggested by Greg, with a president and vice-president both accusing each other of being infiltrated and many branches and regions declaring their own emergency measures. Not healthy for an advanced information society at all. To add to the confusion, the president (and most of the other otherwise quarreling groups) have declared the infiltration as an act of war from the government that seems to be involved with developing and using the nanodevices - everybody is supporting this measure, since not doing so makes everybody think you are an infiltrator.
But don't worry - there are some surprises ahead for the inhabitants of NA (and my players). As for what is going on, I can only say that the plot thickens. Trahan space engineering is a dark horse right now, but a sure tip is Atlantean nanotech startups and selling Dionysian drug stocks. Rumors has it that The Process is in high-level negotiation with the Radical Unificationalists and Balanced Moderators, but how it is going to affect their value after the disaster at New America and loss of the Penglai node is hard to tell. Just some hints for those interested in the current interstellar stock market :-)
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