Flying instructors on the whole want to do a good job, be safe and keep body and soul together, just like real people. What you are suggesting is that the instructor should take a financial hit if you get stuck in a queue for the runway, something the instructor has absolutely no control over.
My staff have the option of knocking off a couple of decimal points from the lesson time when were are stuck behind someone bringing the whole airport to a halt, I usually do, but I wouldn't force the staff to. We don't like being stuck in a queue in 40degrees plus either, while someone sits at the holding point waiting for an IFR clearance from the ATC guys sitting in their air conditioned comfort.
So lets use an analogy. If you were having professional driving lessons, would you want the instructor to "clock off" every time you were at a red traffic light or in heavy traffic? Or do you think the instructor could also use that as a teaching opportunity?
Building these things into the hourly rate is reasonable, using averages from several years operating experience. There are plenty of charges and gimmicks schools have introduced in recent years that I don't think are reasonable and need to be challenged, but paying for engine start to engine stop time isn't one of them.