Areobat
I can only hope things are patched soon to make tampering more difficult. A hardened fix may require a complete change in architecture.
Not sure that would be necessary. All that would be required is a communications gate keeper in firmware that security checks the ACARS/ADS or any other inputs in the same way virus scanners work today. The speed of the scan compared to the lethargic ACARS or ADS would mean that it would not slow anything down.
All these issues will be revisited as the aviation world is dragged kicking and screaming into modern communications systems with Aircraft Access to SWIM (System Wide Information Management). Perversely, in the SWIM world things will be far more secure mainly because it is perceived as a less secure environment and therefore there is no false sense of security.