A control system is disclosed. The control system may have a physical sensor that may output a physical output value, and a virtual sensor network that may output a virtual output value. The control system may also have an electronic control module that may be configured to receive the physical output value from the physical sensor and receive the virtual output value from the virtual sensor. The electronic control module may be further configured to determine a trust level of the physical sensor based on the physical output value, and determine that the trust level of the physical sensor is below a first threshold trust value. The electronic control module may control a machine based on the virtual output value responsive to determining that the trust level of the physical sensor is below the first threshold trust value.