What a great question!
You are absolutely right, soy is a great source of whole protein especially for vegetarians. In fact, when replacing animal proteins with soy, you may even reduce your risk of cardiovascular disease!
Soy is also a controversial source of protein due specifically to it's phytoestrogen content. Some research has found an increased risk of estrogen-dependent breast cancers with a diet heavy in added soy. Yet the totality of the clinical and epidemiologic evidence indicates that traditional soyfoods can be safely consumed by women with breast cancer. Something seemingly evident in Japan and China where soy has been a dietary staple for over 1,000 years. Both fermented and unfermented soyfoods continue in their diets today. Yet despite the high prevalence of soy in their diet, breast cancer rates are far lower than ours.... Confusing?
From the clinical trials and epidemiological studies that I have read the risk is not found when consuming WHOLE soy foods such as edamame, miso, nato, tofu, tempeh, etc. The concerns creep in when we have soy protein isolates added to our food, something that is happening far more than you may have noticed (check out the ingredient statement). Whole sources of soy may offer a healthy syngergistic effect on our bodies, whereas we do not know what will happen by extracting only one piece of the soy (ex. soy protein isolate); this is why I encourage trying to eat as close to natural as possible. While soyfoods such as tofu and tempeh are not exactly WHOLE foods, they include the whole soy bean rather than only the random pieces and parts.
Based on the diets of Asians, Western vegetarians, flexitarians, and omnivores can safely consume as many as three servings of soyfoods per day together with a balanced diet. I simply encourage you to stick with whole food choices and keep an eye on those ingredient statements.
The bottom line: Soy is safe when you enjoy natural whole sources. Just follow in the footsteps of the Asian diet where the average consumption is 1-2 servings of natural whole soy (vs extracted soy protein isolate) (One serving is 1/2 cup tofu or 1 cup soymilk).