I have heard that whey breaks down when heated. I'm somewhat suspicious whether it breaks down at mild heat levels. In any case, you should be fine with soy. Soy is cooked all sorts of ways and is still a good source of protein.
Soy contains isoflavones (aka phytoestrogens) that display weak estrogen-like activity, but I wouldn't worry about it boosting your estrogen levels. Isoflavones also are powerful antioxidants, among having other health benefits.
Soy is not worthless to men. In fact, it's a complete protein (all EAAs present) and is used by billions of people (it's big in Asia). The isoflavones I mentioned above decrease the risk of prostate cancer. It's one of the better proteins. However, whey powder is the best protein supplement for athletes.
So, you don't need to stop using soy immediately for fear of growing a vagina, but I would switch to a CHEAP whey protein powder next time you buy supplements.