The only option Square has at its disposal is to compete with the botters where it counts: gil. Either they offer an officially-sanctioned method of obtaining gil for cash, or the botters continue to provide a service some people pay for.

The only reason bots exist now is there are enough people willing to purchase gil, no matter what the consequences may be to their accounts.

Square meets that need itself, or the "black market" does. There is no third option.