Julie, my take is that if there exists a "preponderance of evidence" for a particular spelling for a particular person, then you may as well use that. It's when you have a grand total of two mentions of a person, each with a different spelling, that the spelling used by the rest of the family makes more sense.
(I've been working on a great-great-grandmother. I've basically entered everyone as Gálfy, although the records vary between that and Gálfi, Gálffi, Gállfi, Gállfy, Gálffy, Gálfÿ, Gálffÿ, and Gállfÿ. I believe I have at least one each of those spellings somewhere, including numerous records where it's spelled one way in one column, and a different way in another column.)