The main reason people use quarantine, at least in my view, is to prevent the introduction of infectious agents into their system in the first place. Basically, a biosecurity measure - as in: an ounce of prevention is worth a pound of cure. It's not perfect as many pathogens can "sneak by", but it decreases the chances of dealing with a disease outbreak in your main display significantly. In the end it's a bit of numbers game. First, if one fish is sick and is in a quarantine tank it's easy to deal with. Introducing a pathogen to a tank full of fish can be very problematic and could potentially exposure your fish unnecessarily to a primary pathogen. Managing and treating many sick fish is much more difficult than dealing with just one. Second, as stated above, most medicines are not as selectively toxic to pathogens as you may think. In fact, most are very toxic to invertebrates, which is a big problem for most marine systems. Others (and there are many) will also kill off the nitrifying bacteria in your filtration system(s). This can lead to a nitrogen cycle in your system and the high levels of ammonia that result may be worse for your fish than the pathogen!
If your fish gets sick after the fact (i.e. after it's been in your main display for while), it's a different scenario. Nonetheless, most of the above applies. It's true that you may leave the pathogen in your system, but it's just the way it goes. The focus should be on the sick fish and the sooner you can remove it the better. However, it's not always practical to move fish out of display tanks (or very difficult) and in these instances you are basically forced to make a judgement call and it really depends on the specific situation as to how best to deal with it.
