The Paleo Diet doesn't prove that killing animals is morally justifiable...

On top of this: the change in demand and in farming practices have dramatically changed and the changes have impacted the environment and the chemical make-up of the produce.
To begin with, paleolithic-era people would have only started developing very simple agricultural farming techniques, and could only grow crops and raise animals that were a) seasonal and b) local.  
Secondly, there is a huge difference between animal husbandry and factory farming.  The fact that thousands of years ago, my ancestors went and killed a ram is pretty different to the fact that today thousands upon thousands of animals will be indiscriminately slaughtered for human consumption.
I think that they've missed the point with the premise of the diet: food is not as nutritionally dense as it used to be - especially food purchased from a supermarket or other source of mass production.  Meat animals are raised and fed differently than they were in the paleolithic era, and therefore there will be a change in nutritional content.  So, unless followers of this diet are going to raise (and kill) all their own produce, and make sure it is as close to 'original' as possible, it's kind of a moot point.
Last, it doesn't change the fact that animals are not ours to (ab)use.  The fact is that we do actually have different moral systems that 'early man.'  I am a bit loath to say it, but we are morally superior, and therefore should be making morally superior judgments.

The relatively small amounts of fat on all these meats would be viewed by modern nutritionists with quite a kindly eye.  Saturated fat, the source of cholesterol with its related contemporary health problems, is a problem of the intensively reared factory-farmed animals of recent years, with their overabundant "scientific" diets and their lack of exercise.  All Anglo-Saxon animals were free range, and the Anglo-Saxons would have been shocked at the idea of ploughing land to produce animal feed.  Ploughland was for feeding humans.  So farm animals were lean and rangey, their meat containing three times as much protein as fat.  With modern, intensively reared animals that ratio is often reversed.