It's a problem because of the aforementioned disproportionate energy consumption.
> "Animals also produce higher quality protein with higher bioavailability"
Hey look, you don't have to pitch me on meat -- I'm basically a carnivore. Personal preferences don't change the underlying engineering dynamics.
> "and provide nutrients that people cannot get from plants."
I love meat and I'll defend it as stridently as anyone, but this just isn't a rational argument. I want meat in my diet, but I do not require it to live. There are many ways to achieve a balanced diet either with other animal products, or without meat altogether.
The really weird thing about diet is that many (most?) of calories a typical American consumes are in excess of a healthy amount and are hurting us rather than helping us. It's a very strange dynamic, because the vast majority of Americans suffer from excess nutrition -- not malnutrition.
These excesses not only hurt our health, they harm the environment. Fat people create far more greenhouse gasses per capita than thin people. I eat meat, but I also eat healthy portions -- which puts me far ahead of most people regardless of their diet in terms of the resulting carbon footprint.