Until recently, cyber-physical systems, especially those with safety-critical properties that manage critical infrastructure (e.g. power generation plants, water treatment facilities, etc.) were considered to be invulnerable against software security breaches. The recently discovered 'W32.Stuxnet' worm has drastically changed this perception by demonstrating that such systems are susceptible to external attacks. Here we present an architecture that enhances the security of safety-critical cyber-physical systems despite the presence of such malware. Our architecture uses the property that control systems have deterministic execution behavior, to detect an intrusion within 0.6 μs while still guaranteeing the safety of the plant. We also show that even if an attack is successful, the overall state of the physical system will still remain safe. Even if the operating system's administrative privileges have been compromised, our architecture will still be able to protect the physical system from coming to harm.