Yeah, some soy products can be pretty processed, like tofu and soy milk.
That's why for meats I go for natural tempeh. It's made with fermented soybeans, and they're still in their whole form. I only have it like once or twice a week though.
I drink soymilk... about 2 cups a week. I don't worry about the processed-ness of soy milk because I drink so little of it.
I eat more wheat than soy, which some people will claim is the cause of many health problems. My cereal and tortillas are wheat. But I don't worry about it because in that cereal, I've got blueberries and sunflower seeds, and in that tortilla is avocado and spinach.
I wouldn't eat tofu every day, I almost never eat tofu. Once I found tempeh, there was just no going back. ;-)
It is possible to have a healthy veg diet with out soy. For me, I could probably do it, but don't because soy is just a convenient source of protein. And efficient too!
For those people who are against soy, maybe they themselves have consumed a lot of it, and so are afraid of potential side effects. Or the estrogen thing... but I mean, to me, it's like... how can you be against the most efficient source of protein on the planet? If there were any one food that could provide every human being with protein in the most resourceful, ecological, sustainable way, it would be soybeans. Only prob is we're feeding half of our soy to livestock.