High quality (grass-fed, organic, free-range) protein is never a problem unless not properly balanced with adequate natural fat and/or green/fibrous vegetable matter. Grass fed meat is not overly acid forming, at all, and is inherently anti-inflamatory (commercial feedlot meat is the problem...even if the grains/corn are organic). Adequate water intake should be sufficient to address the ammonia issue. Proper, thorough chewing and the use of digestive enzymes may be needed (and critically important) to improve digestion and assimilation, as pancreatic insufficiency is also commonly endemic to Autistic spectrum conditions.
L-Arginine may also be used supplementally to assist in ammonia detoxification, if additionally needed, for some reason. You may also want to google "L-Carnosine" or "Carnosine" as an amino acid with great potential in supporting Autistic issues.
There is no one etiology to Autism, though many contributing factors. It takes multiple interventions, normally, to properly address the issue. What is certain is that Autism is a man-made disorder and a uniquely modern phenomenon. It is also interesting to note that no cases thus far have been diagnosed in any Amish community...nor did it exist in any primitive society. Food for thought.
Contributing issues are multifold, including (but not limited to) thimerusol in vaccines (and mercury, in general), food sensitivities (particularly gluten and casein...possibly others), EMF pollution (areas with higher than normal EMF pollution are known to have higher than normal autism rates), prenatal nutritional deficiencies (lending to greater inherent vulnerability), severe dysbiosis and digestive imbalances, severe neurological over-arousal (which may be tremendously responsive to Neurofeedback training) and possibly others. It's a condition for which no one thing is likely to fully correct its symptoms. Steps must be taken to address nearly all of these. M.D.'s are, in general, ill-equipped to address many of these issues and are not remotely qualified to offer nutritional counseling.
Where diet and nutrition is concerned, your son essentially has zero room for error. In general, where there is any severe health issue physically or emotionally my rule of thumb is to adopt a diet as anciently primitive in it's make-up as possible to address it. This means nothing grain or dairy-based (some butter or very heavy cream MAY be OK), no vegetable oils (though olive oil is probably OK), no soy, no processed foods of any kind, only water to drink and never, ever, any sugar. Food should always look like food and be perishable, in nature. Grass-fed (only) meat, organs, wild caught cold-water low mercury fish, eggs (duck eggs can be substituted if chicken eggs are a problem, which they commonly are), fresh colorful vegetables and greens, salads...etc. are all good and important foods. --These are closest to meeting the needs of our universal genetic, evolutionary, physiological design. Added EPA/DHA and cod liver oil (A and D) supplementation is also additionally helpful (as deficiencies are so likely). Green drinks may also be added for their additional antioxidant and alkalinizing benefits.
In the earliest stages of treatment being more plant based may lend itself to better detoxification, since it requires less digestive energy and is so alkalinizing. In my highly experienced opinion, it is a mistake, however, to adopt "plant-based only" diets long term as they are poorly equipped to support neurological function, are prone to generating numerous nutritional deficiencies and digestive issues (such as further suppressing pancreatic function and hydrochloric acid production which, in turn, leads to poor protein and mineral digestion/assimilation). It is important to remember that "cleansing" is NOT the same as "re-building". Extremely high quality animal source foods are far-and -away best suited to re-building and supporting healthy physical and neurological function, as long as digestion is properly supported where needed.