Yes, the soy dilemma is quite disconcerting. The problem is that "bad" soy foods (such as TVP, non-organic, or GMO tofu) release phytoestrogens. This is (basically) a chemical version of the estrogen hormone. Now, it would not be so bad if only soy based food (tofu etc) contained phytoestrogens, but because most of the commercially processed food that the majority of people eat contain soy as a byproduct For men this means lower testosterone levels (FYI - another sneaky source for phytoestrogens is microwaving plastic). There are also correlations between soy and infertility and/or changes to a woman's mentrual cycle. Soy products also activate an enzyme (trypsin), which do not allow the protein to be digested.
In terms of the scarier statistics linked to soy - like thyroid depression and cancer - remember these are correlation - not causalities. This means that eating soy does not necessarily cause cancer, but there is a trend between people who eat soy and rates of cancer.
The key is to look for a form of fermented soy - miso, soy sauce, and tempeh (as you mentioned). Essentially the fermentation process transforms and eliminates the trypsin enzyme. Also, edamame or baby soy beans are also a safe soy alternative, because they are "young" soy beans and do not contain the trypsin enzyme, although they do have the phytoestrogens (less than TVP though).
Ultimately, try to limit your soy to 1-2 servings per day maximum. You should never rely heavily on soy as your major source of protein (as I believe Alicia says in The Kind Diet book). You can google the soy issue, but be wary of scare tactics (i.e. "Why Soy is Evil"). Always consider the source and read both sides of the story. Also, if you're looking for a good meat replacement for chilli try seitan (vital wheat gluten). If you have a gluten intolerance I have seen gluten free versions.
I hope this has helped you!
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