I don't think that everything has to occur naturally for it to be good. There are plenty of deadly natural things. Arsenic is natural, hemlock is natural. We have been influencing the genetics of plants and livestock for millennia through selective breeding. If you have a good gene that can be transferred to a food crop and there are no patent restrictions I think we should do that. Roundup ready is definitely a bad one.

A "good" modification would require:

No patents

No suing farmers that grow your seed without a license/purchase

No boosted tolerance to plant poison

No convenient requirement that "improvements" rely on additional product that the company sells (eg roundup)

Edit: formatting