Sure, we definitely should. But the better way needs to actually be better. TTM is a ton of work, stressful for both the fish and the person. It's debatable on whether or not TTM is any better than copper for ich. Your point about Penicillin is apples to oranges. It was a revolutionary medicine that fell out of favor because many strains of bacteria have become resistant to it do to over use, people are allergic to it and because big pharma is always pushing new drugs. None of that applies here.
If the push for more and more aquaculture continues, this could change very drastically very quickly in regards to resistance.