If it makes the injury heal stronger, what's the big deal? It hurts for, like.. what, a few hours? It's usually only skin-deep.. it's not like they're burning to the bone. (It doesn't look like they use *acid* by the way.. just heat.. acid would pretty much destroy the tendon.)
Don't people stick needles into their skin all the time(acupuncture) to help their health?
Look at it this way-- if your horse hadn't been pinfired, do you think you would have that horse, with him being sound with his bowed tendon?