The list of pesticides allowable in organic farming is (at least under OMRI rules) determined by naturalness, not safety. For example, pyrethrin occurs naturally in chrysanthemums, so it's allowed, even though it's highly toxic to bees. Tau-fluvalinate is a synthetic pyrethroid (pyrethrin analog), so it's forbidden, even though it's sufficiently nontoxic to bees that it's used as a miticide in commercial hives.

Synthetic pesticides are designed and screened in the same way as small molecule drugs, a long and uncertain process that's still far easier than discovering a new natural product. At least in theory, these synthetic compounds can be optimized for whatever we want. It's just that absent regulation, the commercial incentive is for better short-term yield regardless of the ecological cost.

One could imagine a certification similar to organic that forbids the most ecologically damaging practices--even if they're using natural products--and permits safer use of synthetic products. Probably a hard sell to consumers, though. I've occasionally seen produce marketed as "IPM" (integrated pest management), which isn't quite that but goes in that general direction.