Jillaine, I'm inclined to think that you might be confused about the "uncertain" policy. But I suppose that comment might fit me as well. In my opinion, discussing specific examples is a good way to establish rules of thumb.
So, I will quote from the policy and apply it to the present situation, for the consideration of you and others. From the current draft of the policy (I think Chris is still weighing the exact wording):
"An Uncertain name or parent may be speculative but it should not be a guess. If you're only guessing at a name or parent you should not use the data fields. Instead, explain it in the narrative. You can link to highly speculative parents in the text."
That comes from here: http://www.wikitree.com/wiki/Uncertain
The key word is "speculative," which correlates to "conjectural," and conjecture means "an opinion or conclusion formed on the basis of incomplete information." In other words, there needs to be supporting evidence.
In this particular case, I can't see any reason not to conclude that John Stone was, say, Samuel's younger brother or his uncle or his cousin, in addition to the possibility that John was Samuel's father. We simply have no indication of the likely birth year of John, beyond the fact that he was an adult in the 1630s.
In this particular case, "father" is just one of several guesses, so -- barring further information -- John should be detached as Samuel's father. (Samuel Stone is my ancestor, by the way, so I'd be pleased to be able to connect him to the earlier Stone lineage, but there's just nothing there for evidence.)
EDIT: However, as Patricia Hawkins noticed above, "John STONE is named as a grand nephew, son of Rev. Samuel STONE, in the Apr. 17, 1660 will of Rev. Ezekiel ROGERS." So there's the Rogers connection; Ezekiel refers in his will to "my loveing Nephew Mr. Smuell Stone of conecticot", per his will quoted at http://www.wikitree.com/wiki/Rogers-3410
Of course, Samuel's son John can't be the same as the John Stone of Guilford, because Samuel's son John couldn't have been an adult in 1639.