I think it is good to have a mix of automated and non-automated modes of gameplay. Players who value passivity can become crafters. Players who wish to be more active have other options. Automation, and quality of life improvements in general, come with the cost of arbitrage opportunities being transient. Another example is the mall directory idea that keeps resurfacing.
With that said, it may come to be the case that MindArk finds themselves fundamentally incapable of dealing with external program use without creating even more serious problems, such as issuing infractions and penalties to players on grounds of insufficient certainty. If so, then we may have to accept implementing built-in automation as the alternative of least harm among a pool of poor alternatives.