It's not very realistic to eat 100% whole foods, so most people think it's ok to add what is called, "minimally processed foods." This would include things like yogurt, soymilk, bread, cheese, etc. Basically things you could have made at home in the "olden days" or if you lived on a farm having access to your own grain or fresh milk or just plain had more time to make these things, you could do them at home yourself. As Nelie mentioned, you can make your own soymilk and almond milk at home easily. Yogurt too.
As far as yogurt, I don't personally eat that brand you mentioned as it is filled with artificial sweetners which I do not consider a whole food or good for anyone. You can make your own yogurt at home with a yogurt maker quite safely, or even in a pot on the stove. Several of my friends of Russian/Greek ancestry have mother's that make it this way. They basically boil milk, add lemon juice and cover and let it sit in the oven for hours until it turns to yogurt. Personally, I would worry about food safety as I have never done it this way and would stick to a yogurt maker or buying less processed brands. You don't want your yogurt to have corn syrup or artifical sweetners.
I buy Chobani brand and the ingredients are: non fat milk, evaporated cane juice (which is sugar, btw) and vanilla. They then list the cultures they add.
This is my favortie blog about cooking the whole foods way, check out the listing of stocking her natural pantry. http://www.101cookbooks.com/build_a_natural/