I started squatting just a few months ago, and I can't imagine leaving them out of a routine. I think you are 200% correct in doing them in your warmup, whether or not your peers think you are. I think weightlifting can be, at times, twice as psychological as it is physical, and if squatting makes you feel better during a workout, you should do as much squatting as you want.
Yes, hormonal response in limited, but to me it's like icing on the cake, it's just a tiny added bonus that brings you that much closer to your goals.
Even if your legs are getting out of proportion, I agree with B fold, just look in the mirror and say, "fuck, those are some huge wheels" and thank god for big legs. If Tom Platz had stopped training his legs because he thought they were getting too big, he wouldn't have made it as far as he did. If Arnold had said, "I think my biceps are too big, I think I'll stop training them", he may not have been Mr. Olympia as many times as he was