Darwin would certainly have changed his theory if he had known about genetics i.e. he would have known the source of the variation upon which natural selection operates and how it is spread from generation to generation...i.e. he could have scooped the geneticists of neo-darwinism by about 60-70 years.
As to knowing how complex nature can be, that was obvious long before Darwin's time and does not require incorporation of the supernatural to explain it...in fact, nothing in science benefits from incorporating or postulating mythical supernatural causes.