No, I don't think Marjory and Elizabeth have ever been considered to be even remotely related.
Margery/Marjorie (etc.) was originally a variant of Margaret, but was used as an independent name as early as the 13th century, to the point where a mid-17th century writer derived it from the name of the herb marjoram.
Elizabeth, of course, is known for its great proliferation of diminutives in English, some of them with little to no obvious connection to the original: Eliza, Lizzy, Betty, Betsey, Tetty, Tetsy, Beth, Bess, Elspeth, Elspie, Elsie, Libby, Tibby. It shares its derivation with Isabel, which the popular naming pool ignored from very early on, but which sometimes caused confusion when scholarly-types used them interchangeably.
I suspect the difference in the bride's name is due to either a misreading (possibly of an abbreviation) or a double given name (which would've been extremely rare but not totally impossible in 17c Scotland). There's also the possibility of an error (typo) in one of the books. I don't know anything about Scottish recordkeeping, but the best way to resolve this would seem to be to track down the marriage record that the books are citing?
(Name derivations etc. based on E.G. Withycombe: The Oxford Dictionary of English Christian Names, Third Edition, 1977.)
