RDP, you’re a brave man if you talk to scientists about philosophy!  
The word ‘natural’ in NL seems to be the source of some confusion.  NL does NOT mean that you can find morality by the scientific study of nature.  It does NOT mean that biologists can tell us what is or isn’t moral.  Rather, it’s the concept that rational analysis can determine what’s morally good and evil.  That is, we don’t necessarily depend on revelation to tell us what’s right—pagans, by applying reason, can also come to a correct moral understanding and that this understanding is universal.  It has a teleological aspect (ie, it assumes things in the universe have a purpose) and generally assumes a  Creator God.
I’m curious why you think ‘this idea should be thrown out all together by the Church for any explanation of morals or ethics.’   Why is that, and what alternative do you propose?