Geralmente é difícil provar um negativo. AFAIK, não há como descartar completamente R + L = J. O único recurso é examinar os argumentos que sustentam a afirmação de que Ned Stark é de fato o pai de Jon. E esses argumentos foram resumidos na pergunta que você citou:
Reasons to affirm that Eddard is Jon's father:
In the aforementioned investigation by Catelyn, a recurring rumor was that the mother was Ashara Dayne. It is implied by other flashbacks (principally the story of the Knight of the Laughing Tree) that Ashara and Eddard shared a mutual attraction.
When pressed by Robert, Eddard claims the mother is a servant girl named Wylla. Edric Dayne claims to Arya Stark that Wylla was his wet nurse (making him Jon's milk brother), giving more credence to the story, and that Wylla was not just a name Eddard made up to shut people up.