Is it the artificial selection of the best breeding stock you object to Heidi or simply queen rearing methods? I ask because I don't see organic or biodynamic farmers applying that kind of thinking to any other animal in their care. You won't let any old bull run with the herd. There probably wouldn't even be a herd unless countless generations of farmers had bred from the best, according to the things that were important to them.
There was an old bee farmer in Shropshire (now deceased) who used to just split his best colonies in half in the autumn and let them rear their own queens. The best ones being the ones that produced the most honey. He had some good bees.
There is growing evidence that epigenetics play an important role in colony health, that is the passing on of the genes of all the organisms co existing with the colony, not just the genes of the bees rthemselves, so splitting your best colonies will also propagate all the healthy beneficial microbes essential to colony health.