While there is an issue regarding warranties and engine damage derived from tuning the motor, there are other things at stake that always give me pause when I get too riled up about these. Modern PCMs have access to so many functions on the car including power steering, braking, throttle, suspension tuning, etc - many of these functions for safety.
People could certainly (by accident or maliciously) change those systems in such a way that they no longer function or, even worse, malfunctions during normal driving. A funny example of this is the CTS-V that had OnStar go off thinking there had been a wreck because it accelerated so hard - think if a similar incident makes a car think there is an impending wreck and it pre-brakes and sets off secondary airbags or any number of other systems.
Integrated systems behave in weird ways when variables are changed outside of their normal operating specs. Manufacturers should be prepared for this, but all it takes is one bad series of events and they will most certainly be named as culpable in the lawsuit.
As someone with HPTuners and a mind for tinkering, I'd hate to see a world where we can't do that. As a realist, I know that time will be here eventually, at least from a legal standpoint.