Circumventing the technical protection measures on nanofactories would require a certain level of privacy. While efforts have been described to make the operation of nanofactories a published event through the use of Internet connections, the most obvious step to make a nanofactory's operation public record is to actually require that the fabs themselves be installed in public spaces, and monitored with video and audio surveillance in the same way stores are today.
Safeguards against removing the machines from the surveillance zone would be straightforward, given super-strong materials. Circumventing the surveillance mechanisms could be made difficult with redundant surveillance (multiple, cheap cameras throughout the zone), making a sophisticated information attack necessary to substitute "spoofed" video feeds, as well (simply disabling the surveillance is easily detectable).
The idea is to turn nanofactories into BUILDINGS, so as to make stealing one for study a trivially detectable and absurd endeavor.
Since fabs would be as easy to replace as they would be to repair, there is no need to maintain or repair a failing fab. Thus, there would be no need to service it. This would eliminate the possibility of an attacker posing as an authorized fab technician.
When production becomes a public act rather than a private one, it becomes accountable.
Nanofactories the size of buildings...technically, it's quite feasible, and the consequent simplification of security issues is attractive. The factories could be widely distributed, to be no further, perhaps, than one hour's travel (or even closer) for 90% of the human race. However, this approach still requires the existence of a global authority overseeing the creation of every new nanofactory as well as approval of all available product designs.
It's an idea that should be thoroughly debated and studied.