It's the legislature's place to make that decision. The companies don't get a pass on breaking the law because everyone's doing it, the same way you and I don't get a pass.
And I don't think every company is breaking the rules. Letting the scofflaws off sends exactly the wrong signal to the companies that made sacrifices (in price or performance) to stay within the law.
Not sure I understand this logic. Certainly everyone is not cheating emissions regulations. Some vanishingly tiny proportion of humanity (0.0001% of people or less) are responsible for cheating emissions regulations, whereas all 100% of us have to breathe in the resultant harmful pollution.
You're trying to compare this to jaywalking or something, but it isn't. Laws are passed by and for the benefit of all of humanity, so you must look at the entire group of all people. You can't just narrow it down to automobile manufacturers and say that if they all do it it's right, because there is more to society than automobile manufacturers!
Tons of people litter, but it's definitely a good idea to have it be illegal.
Besides... This rule is not crippling. These companies absolutely could have met emissions just by keeping the engine in test mode. Not only that, but they could have just not made deisel cars. They broke the law because they didn't want to settle for a tiny inconvenience, in a market they didn't need to be in, selling cars to people who would have gotten a gas car if they had to. The sheer arrogance necessary to convince themselves to blatantly cheat on an emissions test (by detecting test conditions and gimping the engine) is staggering.