Humans have been processing foods for centuries. However, the issue is often how they are processed and why. Soy can be good if it is processed correctly, but that processing takes a lot of time. Tempeh production, as far as I know, does not command the mainstream credibility of soy milk. Lactose intolerant people and people with milk allergies often mistakenly choose fortified soy milk as a substitute for milk. This is especially a great folly if one is from a culture which consumes a lot of dairy. How would one manage to be lactose intolerant in a dairy-heavy culture? It does happen even to those people who have no mixture with other races or even ethnicities however rare it may be. With the rise of people in the United States mixing even within the Caucasian race, we see hybrids either having or lacking lactose and milk tolerance. There is your correlation with a rise in soy-as-dairy use along with the health food crowd. Many cultures consume fermented dairy: many cheeses, yogurts, and butters are cultured which enhances their digestibility. Look at your other options before you drink and eat yourself beyond womanhood as the danger of soy is not just in milk. Anything with vegetable oil, for example, is likely contain some soy as soy is also used as a crop for cooking oil.
Whole grain is not going to kill if you if your body is adapted to digesting grain. White grain and white sugar are another story. Calcium can be found elsewhere if you need it, but get used to consuming shells, bone, etc. in various forms including broth or stock for soups. Beans are great for protein and tasty if you season them properly.