The biggest deterrent on modifying the ECU is the warranty voiding. The average person isn't going to risk voiding the warranty on a brand new vehicle. The small percent of people tuning cars doesn't eat into the manufacturer or dealer profits so it's not really on their 'radar'.

No one will ever be able to stop tuners doing what they do. Modern vehicles are nothing more than a computer with wheels and an engine. Like any computer, it will be hacked / datamined / reverse engineered. Even if "kill switches" (that's still a big if) are even implemented there will almost certainly be defeats.