Regarding humans being a part of nature or not, we can never escape the effects of nature, so why should we say we are not part of it? We may think we are making huge differences by polluting the world and driving species to extinction, but nature includes the entire universe in my definition. Anything we do is like moving one molecule of silica on the smallest grain of sand in the Sahara. It simply isn't significant in the whole scheme of things.
In my opinion, we cannot control nature to a very large extent at all. Look at what we have available now to control the world. Sure we can increase the average global temperature, but nature can do that too. If we were to fire off all the nukes we have in possession now, the earth would hardly notice. Life wouldn't notice either. Individual living things would, but life as a whole would not. We can try and kill every living species on this earth, but we will always miss something. There is basically nothing we can leave behind that nature won't eventually erase. We can totally isolate ourselves in a sterile chamber for the rest of our civilization, but as long as we have a biology, nature is going to win. Aggression and lust are always going to be present and causing problems. The very fundamental part of our psychology is rooted in the struggle to pass on our genes.
If we went extinct tomorrow, life wouldn't care at all. Sure all the cows and other domesticated species would go extinct, but life doesn't care how many species there are as long as some piece of DNA somewhere is being replicated.
In fact, it is the probably the simplest organisms that are fittest of all. Some have "learned" to exploit us for their benefit. Bacteria in our body outnumber our own cells by a billion I think. They will go wherever we go, and if we die, they can go dormant and wait for another host to pick them up. We can't kill them because they are essential for our survival.
I think the biggest misconception people have is that natural selection and survival of the fittest works for the group as a whole. Your genes don't give a darn about any other living thing as long as you can pass on your genes. It is IMO wrong to think of any species manipulated by people as being detrimental or unfit, because from the point of view of their genes, if the animal is reproducing, the "point" of the animal is being fulfilled. Whether we like it or not, the "point" of a wolf is not to hunt smaller mammals to keep their populations in check, it is to reproduce its own genes.