Has the character of Miss Moneypenny in the movies Skyfall, or the upcoming Spectre, been altered at all from its source material (the Ian Flemming novels)?
She's very altered in the films.
Miss Moneypenny, in the books, is the private secretary to M. She is completely dedicated to her work although she tends to mildly flirt with James Bond. She appears to harbour genuine affection for him too, although never states this As the Wiki for her comments:
In the novel Thunderball, Fleming wrote that she "often dreamed hopelessly about Bond." However, she never explicitly voices these feelings.
However, in the books she's not a big character. Bond actually has his own secretary, Loelia Ponsonby (who is also secretary for 008 and 0011). When she retires, Mary Goodnight becomes his new secretary (appearing in On Her Majesty's Secret Service, You Only Live Twice and The Man with The Golden Gun). In the final novel, her role is expanded and it is hinted they may have had a relationship (or affair of sorts).
Given the prominence of Bond's secretaries, Miss Moneypenny is very much a background character, albeit one with affection for him.
In Skyfall, Miss Moneypenny is obviously shown as a field agent for a time. This never happened in the books. Also, in the film Octopussy, she is shown with an assistant, Penelope Smallbone. She warns her assistant about the dangers of falling in love with Bond - again, this never happened in the book. In the books she simply has no back story.
As for her appearance, if I recall Miss Moneypenny is never physically described in the novels. She simply makes an entrance as "M's private secretary". However, given the fact the many possible candidates that the character was based on are young, white women, it's likely her ethnicity is a change from what was originally intended in the novels.
On a final note, if you are interested in Miss Moneypenny, there was a book released in 2005 (2008 in US) called The Moneypenny Diaries: Guardian Angel. It's the first of a supposed trilogy of novels about Miss Moneypenny, written by Samantha Weinberg. They are officially licensed James Bond material, so in theory are a form of canon (although probably not as canon as Fleming's original work).