re: Is it acceptable for me to punish junior high(7-9 grade) kids for a loss?

Do you spend time shooting free throws every day in practice? Maybe you should look at how much time you spend doing it or how you coach them. I would not run them. It is your responsibility to get them ready in all facets of the game. If there is a shortfall (other than athleticism) then that is on you. How does running fix their shot?

Fix the problem...it is your problem too. Running them says "it's your fault" to the kids on something for which the lion's share of the blame is yours. Be a man and take responsibility for the problem. Then do your job and fix it. Run them for stupid mistakes that they have been coached and coached not to make.