[Shadow of Udûn]

I don't think that Tolkein was saying that nature was always fantastic. I think he was just as interested in showing it's brutality, as well as it's incredible beauty. Mount Caradhras, for instance, is almost a living thing, which seems to delight in thwarting the Fellowship's passage. And, after all, Mount Doom is natural. Certainly Tolkein was writing about nature in a wonderful manner, but he was also saying that nature can be brutal as well as kind.
Then again, perhaps that's a moral. Elve's live in harmony with nature, and their lives are care free and happy. Orcs, the very opposite of elves, live in conflict with nature, and each other, and live lives which are described as pretty miserable. Sauron twists the earth to his own uses. Tolkein probably wasn't a conservationist in the modern vein, but he was certainly giving a message about what happens when we don't live in harmony with nature - that we can't live in harmony with each other.