Did you read the article? This was not a case of "fixing their car" this was a 4 million dollar business selling illegal services to disable emission controls. They absolutely deserved to be prosecuted.
I read the article, and I've read about these cases over the past few years. Many of the emission control components degrade engine performance, decrease gas mileage, and decrease reliability. The EPA kept moving the goalposts and went beyond the limits of practicality. Congress did not set the limits, so the EPA was basically making it a federal crime to circumvent their rules (not laws). Who do you turn to when the vehicle for which you've paid upwards of $100k doesn't work right, and cannot be made to work right as designed?