Any form of engineered design is unlikely to go backwards in terms of the functionality and flexibility that things like bus communications bring, but awareness of these new attack vectors needs to be included in the base design.
This is the path that industrial control systems are taking in light of attacks such as Stuxnet, I expect that the automotive guys (who are usually ahead of the game in terms of systems engineering) will follow suit.
Edit: The problem I have with people proposing air gaps and read-only circuitry, is that they just don't work in real applications. If there is a business case against it, such as the service these jeeps were offering, then air gaps and hardwired circuitry solutions will be overridden by that business case. Further than that, as can be seen with things like the Lenovo hardware fiasco, manufacturers cannot be trusted to abide by the rules (such as: air gaps are now mandatory), when there is a benefit for them to act otherwise. As Chrysler now has the ability to remote into their cars, they are very unlikely to remove this ability 'merely' due to safety concerns.
It's far safer on the whole to offer secure methods of achieving the existing or proposed functionality, than to try and walk backwards and make things harder and more costly to implement, for lesser functionality.