Some searching of patents by Orbital Sciences Corporation will reveal a patent from 2009 describing "A secondary payload interface for payload communications using a primary payload communications channel is provided." This is essentially a space version of a radio repeater or WiFi range extender - and also provides for a redundant communications network to ensure that remote controlled spacecraft and satellites can remain in constant contact with ground control.
The patent discusses the potential for using communications satellites to relay commands remotely:
Although typically built with that single purpose in mind, these satellites may provide platforms for secondary payloads. For example, communications satellites can provide power, thermal control, and attitude control system (ACS) functions, as well as other services, to secondary payloads, such as, for example, earth-observing or weather-monitoring payloads. An auxiliary high rate communications system can be provided on the communications satellite to accommodate the secondary payload.
And good news! The patent is designed with security (encryption) in mind!
In some embodiments, the secondary payload interface may be designed such that control and telemetry interactions with the operators of the primary payload and/or the host satellite (which may be the same or different) are limited. For example, control interactions may be limited to power connections. As another example, telemetry interactions may be limited to discrete telemetry points that provide insight into the basic health of the secondary payload interface. As a result, the secondary payload may still be securely controlled by its operator without involvement by the operations center of the primary payload and/or the host satellite. This approach provides segregation of signals between an encrypted state and a non-encrypted state (e.g., a "red/black" interface) as required by some encryption systems.
A second possibly related patent by Orbital describes "Emergency Communications Channel Systems and Methods for Satellite Command". This patent can be accessed here.
This patent creates a backup system for satellite communications - ensuring availability of control if something goes wrong with traditional satellite communications.
To address [...] shortcomings within [remote satellite control], an Emergency Communications Channels (ECC) satellite command system according to one aspect of invention enables commanding of a satellite by remotely modulating telemetry data parameters indicative of the operation of one or more of the satellite's payloads by modulating signals sent directly to the payload from a ground station.
The two above patents definitely show that Orbital understands the importance of implementing security and redundancy in space systems - and is actively implementing important security concepts in their spacecraft and launch systems.
I look forward to discussing this topic further with them when I visit NASA's Wallops Flight Facility in a few days.