It was never explained why that name has chosen. Certainly there has been speculation on that, though. One idea was because it has the letters M & G in it (Michael Gregson's initials). But it certainly would not have been my first choice.
Edith and her romance with Gregson have been compared to Jane Eyre, so maybe Jane might have been a good choice, or Charlotte. Adeline might have worked too (the first name of Virginia Woolf, whom Gregson introduced Edith to).
In England, certain types of female names are fairly traditional. You have names with classical Greek or Roman allusions (such as Diana, Camilla, Julia), which tend to be more aristocratic, while naming a girl after a jewel (such as Ruby or Beryl) is much more lower-class. However, the most traditional names of all for girls are flower names, and those are popular both in the upper and lower classes. Note that in Downton Abbey you have the aristocratic Violet and Rose (who is played by a woman named Lily!), while downstairs you have Daisy, Ivy, and Rosamund's former maid Marigold Shore. I suspect Marigold was chosen as a name for Edith's daughter for the same reason it was chosen as a name for the maid -- it is the sort of name that might be given then in any class. (And by the way, did you know that Winston Churchill, who was the grandson of a duke, had a little girl named "Marigold", who unfortunately died at the age of three in 1921?)