I don't want to run brood through the extractor either. I don't use excluders BUT because of the frames being interchangeable, I can move brood down, and honey up. There is a tendency for the bottom box, at least here it seems a tendency, to plug completely with pollen. That effectively limits my unlimited brood nest, and until August, I want big monster colonys to make big monster crops. The honey cap many times works as an excluder and keeps the queen from moving up into your supers. If she still does, whats the loss? A frame or two? Pull the outside frames on the next box down (almost always full frames of honey}, kick the next two out, and move the brood down. Viola.. a full deep to harvest.