Much of this concern has evolved from misleading information about soy. There is zero evidence showing that horses are allergic to soybean meal, soybean oil, or whole roasted grounds soybeans.
Blood tests commonly used for diagnosing allergies are not a reliable diagnostic tool according to experts in the field. Board certified experts in the field lack confidence in blood tests and recommend skin tests instead. Granted, skin test are expensive and require an expertise other than general practice.
You may have heard about trypsin inhibitor as it relates to the trypsin enzyme. Proteins are too large to be absorbed into the blood stream and several enzymes are responsible with breaking down the proteins into smaller ones (peptides) and to the amino acids. Trypsin is one of those enzymes that is produced in the pancreas, released into the gut and has a specific job in the digestive/preparation process of protein.
There is a trypsin inhibitor in raw soybeans which is why a standard and common practice is to roast the soybeans prior to use and formulating in animal and human foods. The roasting is at a fixed temperature and time period to denature (destroy) the trypsin inhibitor. around 1000 lbs, then feeding 1 ½ lbs of Integrity Lite will work, or feeding half the amount recommended of a generic vitamin/mineral horse supplement.