At the moment, my working conclusion is that ultimately, the link to Rev. Samuel Rutherford and Rev. Joseph Alleine is derived from McPheeters.
McPheeters cites Joseph Walker son of Katherine as his source.
But he does not say exactly what came from Jospeh. I'm willing to grant that its likely that Joseph knew who his grandfather was, passed it on to McPheeters, and that McPheeters probably got that right when he identified him as John Rutherford. But deeper than that, I don't think you can give him a get out of jail free card. McPheeters didn't quote Joseph, or cite a letter from him, etc. As a result we don't know what he specifically learned from Joseph. In particular we don't know if what McPheeters had to say about the Alleine's and the Rev. Samuel Rutherford actually came from Joseph. It might have been something that McPheeters figured out on his own. if so, he might have figured it out correctly (based on what we don't know) or he might simply have been guessing. Based on what evidence can be pointed to, I'm inclined to think that McPheeters arrived at his conclusion that Katherine was related to Rev. Samuel Rutherford and Rev. Joseph Alleine, based on "must be" kind of thinking. That is, he saw the Rutherford and Alleine surnames, and guessed that they must be related to the well known divines. In anycase, there is no evidence that this connection was made through his conversations with Joseph Walker.
McPheeters makes no mention of Isabella Alleine. So White's reference to Isabella presumably came from some other source. Her sources for that information probably included the Joel Walker Record. Joel wasn't descended from John Rutherford and Isabella Alleine, based on DNA evidence---so in this respect, his record is tainted. Since he didn't get his own connection to the family correct---why should we believe the "deep part" of what he tells us? (That assumes that his record indicated a connection to Isabella Alleine in the first place). We do have, however, another source for White's identification of Isabella Alleine as the wife of John Rutherford..... need to insert comments from Mrgaret Walker re Isabella Alleine
In her forward, White makes reference to a manuscript left by the father of the Rev. Samuel Rutherford Houston. That MS was probably the basis on which Houston, 1882 was written. The MS itself, however, does not seem to have survived. White quotes a brief passage from it (see White's Comments on the Rutherfords),....This needs work