Soya has important phytochemicals that have significant health benefits beyond simply being a source of protein in our diets. Soya has high levels of phytochemicals and is know to prevent cancer and cardiovascular disease.
Adverse nutritional effects or other effects as you mention following consumption of raw soybean meal are due to the presence of endogenous inhibitors of digestive enzymes and lectins and to poor digestibility. To improve the nutritional quality of soy foods, inhibitors and lectins are generally inactivated by heat treatment during food processing.
The soya available in the market is heat treated and safe to consume.