Back to the article, I think that this type of exploit will become more and more common as vehicles become more connected and automated. We need to know that we can trust the software and firmware running on the devices that literally have the power of life and death over us. Unfortunately, this is a VERY complicated issue, and no one has a solution yet AFAIK.
I watched a talk by Cory Doctorow last year where he suggested validation at the hardware level (a la trusted platform modules), but unlike the typical TPMs that only allow vendor software to be authenticated, these TPMs would allow the user to directly authenticate the firmware. If you know the firmware is good, then each layer can validate the next layer up all the way to the OS.
I have yet to hear of a system that allows the user to directly authenticate software/firmware at the hardware level. Is anybody working on research of this nature? Or are there insurmountable problems with this approach?