This paper proposes an energy-efficient security-aware architecture for wireless control systems to be used in factory automation. We face deception attacks that corrupt commands and measurements in a smart way and with intermittent behavior to produce the highest damage without being discovered. The intrusion is hard to distinguish from normal disturbance. Furthermore, protection against attacks is energy-consuming and it would be desirable to activate protection only when needed. We propose packet-based selective encryption to reduce energy consumption, and to detect when an attack starts and ends. Since energy consumption depends also on packet transmission rate, especially during attacks, we also propose to adapt it according to instantaneous control performance.