You are correct! The long term benefits of disease for an ecosystem would not be present in a tank. I think an argument could be made that a fully quarintined system will be far more susceptible to disease in the rare instance that a disease gets introduced.The wild ecology of diseases doesn't apply to captive marine systems. No marine organism should have an immune system reliably capable of tolerating rapid and repeated disease in a marine tank.
I'm not arguing that proper quarantine isn't better than not. However I do think that anyone who improperly quarantines or doesn't quarantine everything (like if a disease got into to a system that has been quarantined for a long time) may be more likely to have a wipe out a tank than someone who doesn't quarantine at all. I also worry about coppers long term health effects.
Either way it's a complicated issue. And either way I'm buying my fish pre-quarantined or captive bred anyways for reasons I said earlier.