Hunter-gatherers did not have too much protein. I seriously doubt that they could eat meat everyday. They'd probably eat wild grains and fruits too. They only had adequate amount of proteins in comparison to the first farmers. Then, the first farmers did no grow vast amount of different vegetations nor do they domesticated animals. Both had not been discovered yet. They would have to rely on one or two major plants as the primary source of food. Since they spent all day on farming, they wouldn't have the time to go looking/hunting for other fruits and vegetables. That would explain why the hunter-gatherers have better health. Yeah, you are right about the types of amino-acid contributing to the health. The first farmers rely on a certain plant that doesn't have all the essential amino acids. As the result, they have malnutrition. However, human can synthesize the nonessential amino acids if they are provided with any amino acid. One has to have enough protein everyday. According studies, a 70-kg man needs a minimum of 20 grams of protein. A slice of bread has 2.3 grams of proteins. It will take 9 slices of bread to achieve it. On the other hand, it takes 1 or 2 serving of beef to achieve the same among. When there is meat, the hunter-gatherers would finish the entire animal because there is no refrigeration. If that is the case, they should have more than enough proteins for muscle growing. The farmers would not have enough proteins for that. The hunter-gatherers would have a better chance of getting proteins quantitatively and qualitative. They should be healthier.
Finally, I think the distinction between Hunter-gatherers and farmers are not as strict as described by the original author of the webpage. It can be mixed. For example, in a tribe, men went out to hunt; women were left in the village to farm. The author over-simplifies things to begin with.