Watch this video on Stuxnet.
I suppose the answer, for systems that can justify the additional cost, is not to use standard off-the-shelf hardware. The people who built stuxnet knew the details of the Seimens SCADA systems that run the centrifuges. They would also know the details of the centrifuges. Iran, like Pakistan, does not have the capability to build centrifuges. (India's nuclear programme, I think, does not require centrifuges.)
Not using standard hardware and firmware means building them in the country. Good news for Indian engineers.
Safety is one dimension of embedded software quality. Safety includes security against malicious attacks. Watch this webinar on security in eHealth.
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