Soy protein doesn't mess with anything. It is perfectly safe. I eat all kinds of soy and I'm still alive and healthy..This article
notes that soy protein has benefits for dieters looking to maintain muscle mass:
For years, bodybuilding gurus have recommended the use of soy protein for pre-contest bodybuilders who need to shed body fat while keeping as much lean muscle as possible. Normally when the body is forced into a low calorie diet program, it reacts by slowing down your metabolic rate. This will make it increasingly more difficult to lose body fat. Soy-protein isolate helps lessen this effect through several different pathways. First, soy-protein isolate has been found to enhance endogenous production of thyroid stimulating hormone (TSH), thyroxin (T4), and triiodothyronine (T3). Thyroxin is the main player in the regulation of your metabolic rate. The more thyroxin you have the faster your metabolism will be. A faster metabolism insures that more of the food you eat will be used as fuel and less will be stored as fat, an important advantage to any dieter.
Another way soy accelerates fat loss is with its unique concentration of amino acids. Soy-protein isolate has the highest concentration of amino acids in what is called the "critical cluster". This cluster of amino acids contains the three branch chain amino acids (BCAA's) and two essential aminos - glutamine and arginine. These critical amino acids help a bodybuilder spare muscle while losing body fat during a pre-contest diet. Any time you diet, your body tries to break down muscle glycogen in an effort to provide the body with more calories. In fact, your body will often try to use broken down muscle for fuel before it uses stored body fat. This is called muscle catabolism or muscle breakdown. These three branch chain amino acids are the first amino acids that are used for fuel when your body begins muscle catabolism. If you have a high amount of these branch chain amino acids in your diet, your body will first use these for fuel before it breaks down your stored muscle.
Read the whole thing, as they say. Especially section 6 -Soy Protein Isolate benefits for Bodybuilders.
PS - most meal replacements and whey protein powders are fortified with glutamine to boost their utility. The most common source? Hydrolyzed wheat gluten:
Let me share a little known fact about some of the products out there in the supplement marketplace today. Have a look at some of the labels and you will see companies touting something called "Glutamine Peptide". Sounds high tech right? Actually Glutamine Peptide is an industry term that really has limited meaning. Glutamine Peptide by definition is L-Glutamine, peptide bonded (a chemical bond between two amino acids) to another amino acid or several other amino acids in a chain (protein). Within the supplement industry Glutamine Peptide means . . . . wheat protein. What’s so great about wheat protein? It is about 37% Glutamine compared to whey protein, which averages between 6% to 10% Glutamine.