Nature gods don't like overuse of it, they are fine with you using it to turn barren land fertile, but they get angry if you use it to plunder the land, by growing only high yield plants that suck all the nutrients out of the earth, and then using it to fix it, or that's how I read it, nature gods are okay with using it to make land fertile, they are not okay with using it, to avoid the consequences of unbalanced farming.
The spell specifically say overuse angers high level druids and nature gods, not that using it anger them, so I take that to mean that they are fully onboard, with using it to return life to infertile land, but they are not okay with people exploiting the land until it becomes infertile, and then using the spell to make it fertile again, if you do it once they wont come after you, after all you might have just been ignorant, about what your farming methods did to the land, but if you repeatedly farm the land into infertility, just to rely on magic to make it fertile again, they will come and punish you.
They will also come if you follow Goldfish plan and use it with Womb of the Earth, or at least if you rely on doing so, they will probably forgive using Womb of the Earth and Enrich soil once, but if you do it regularly, they will see you as exploiting nature and punish you.