That's not really sound logic - if you see a yellow light and there's enough time to safely stop, you should stop. That's an important qualifier. Indeed, that's why the duration of yellow lights differs based on the expected speed that people will approach them - because it's not, in fact, always safe to stop when you see yellow. (As a thought experiment, ask yourself why we have yellow lights at all, and why they're not instantaneous).

What the city did in this particular case was deliberately shorten the yellow light to a lower time than is actually legal or safe - just to make a few extra bucks.

Now, if your argument was more that "well, the city's wrong, but most of the people who ran the lights are still guilty", then the argument is really similar to the one about the exclusionary rule (evidence in criminal cases can't be used if obtained through an illegal search). Without some way to punish the city, there's no disincentive for them not to keep screwing over people - in this case, in a way that actually increased the accident rate. There's got to be some pain felt for malfeasance, and it sounds like that's exactly what's going on here.