I hate long yellows, and even worse is the "all red" period some cities have added between the yellow and the next light turning green. It makes traffic inefficient for people who follow the law (which says you must stop at yellow lights) and it vastly increases the number of people who blow late yellows and even reds.
All-red periods are also useful at intersections where traffic backs up and blocks the intersection for a few seconds, not because drivers entered the intersection when traffic was stopped, but because events down the street or at an adjacent light may cause traffic to stop suddenly with drivers already in the intersection.
I don't know about where you are, but here amber lights mean "Stop if it's safe to do so", i.e. if the choices are go through the junction or slam on the breaks, you should go through the junction. If the choices are to stop smoothly and safely or go through the junction, you should stop.
And I disagree with your justification for all-red periods. If you're stopped in the middle of an intersection because of a blockage, it usually takes a lot longer than 1-2 seconds to clear the intersection.
http://beta2.tbo.com/news/nation-world/2008/mar/12/na-red-li...
These systems are usually run by contractors, who include a guaranteed-revenue clause in their operating agreements. If the cameras are actually effective in stopping people from running red lights, then the operators will go back to the local government to demand that they make up the shortfall.
All in all, a dirty business that's clearly not safety-driven.
http://blog.motorists.org/6-cities-that-were-caught-shorteni...