I dispute the validity of comparing headers to the helmet-to-helmet hits made by American football players like Junior Seau and Aaron Hernandez. Those guys weigh over 200 pounds, are running at speed at the time of the impact, and are intentionally trying to deliver hard hits to the other guy. They will have body and head impacts 30 times in a game or more. By comparison, a properly-inflated soccer ball is a softer body in motion, weighing slightly less than a pound, and flying at a predictable trajectory. In a professional game, a typical soccer player may only head the ball 2 or 3 times, and most of those balls are not moving very fast. Obviously, free kicks, punts and hard driven balls like crosses have greater energy.
While I respect your concern about the potential for CTE in soccer, I think you greatly overstate the risk insofar as headers are concerned. Again, most soccer-related concussions are caused by other types of contact with the head. Personally, I have never seen a concussion arise from an intentional header, though I don't doubt that it could happen. And while I agree that too much practicing of headers is unnecessary and unwise, I have never personally met the coach who spends the amount of time practicing headers as you describe.
If you are concerned about headers, then your child is already 12 years old or above. If the science catches up and says that headers cause CTE, that won't happen for a decade at least. Your son or daughter will have aged out before then. If you act according to your beliefs, then you must tell your child not to do headers in practices or games. This will have consequences. Your child will not be able to play competitive soccer during his or her youth unless he or she is willing to head the ball. Others will take your child's spot in the line-up.