Mankind becoming more knowledgeable and rational is also a "natural" process. Why draw a distinction at this point? It is perfectly natural for a species to reject superstitious and religious ideas as its intelligence develops.

Natural does not mean good. Nature often needs to be defied for our benefit. For example, medicine.

Evolution does not produce a perfect species. Just because something evolved a certain way does not mean it is a good thing. There are many vestigial and maladaptive traits, such as our desire for fatty/sweet/salty foods that served a purpose when food was scarce, but now causes illness.