This NYT opinion piece teaches us two things: (1) scientists can be ideologues; (2) just being a scientist doesn't mean that you know what you're talking about.
The main problem with Ellis' analysis is that the historical fact that we've remade the planet on some scales does not mean we can do it at all scales. We've terraformed the Earth's land ecology for agriculture, changed the ocean by hunting whales to near-extinction, and industrialized and urbanized to regionally change much of the landscape. Those things are big, but they're not at the global and geologic time and space scales. Ocean acidification, climate change, ozone depletion, are planetary scale changes. We are literally creating a different planet than the one we evolved to live in. We cannot transform the Earth at this scale and still have a planet that we would want to live on.
The other problem with this analysis is that the largest environmental challenges we face (indeed, the largest challenges we've ever faced) aren't things that we're doing on purpose. (Ellis lists as an example the revolution in agriculture.) It's the fact that we're fundamentally changing Earth's atmosphere, oceans and climate in unintended ways that is the big problem.
And of course, both the scale and scope of these unintended environmental changes are correlated to world population growth.