The thinking is that if the medication is any good (ie potent) then it will kill more than just the target parasite. The reason these treatments are "reef safe" is because they are so weak that they don't kill anything - including the parasites - in significant quantities. Hence long expensive regimens.
The prefered method is to isolate the fish in a QT
, leaving the main tank fallow for at least a month. Then use hyposalinity to treat the fish. Over the course of the month the parasites will completely die off and you can return the fish to the main knowing that you'll never get any ich again. Providing ofcourse you QT
all new additions first.