But the risks that running a red light pose aren’t civil in nature, so it feels like a perversion to use civil infractions as an excuse to get sloppy with enforcement.

The alternative would be an actual criminal record because you misjudged a yellow light.

If the yellows are set correctly there should be very little of misjudging. You see yellow, if you can reasonably stop you do so. Judging only is an issue when you're going below the speed limit.