Molly was indeed the original name for Amy. Chris is also named "Bob" in these summaries.
The initial publicity materials actually went out with Amy and Chris identified as Molly and Bob, and, strangely, even after the characters had appeared on the show, several magazines continued to identify them that way. Here are just three examples:
(http://www.dsboards.com/images/cast-1.jpg)
(http://www.dsboards.com/images/cast-2.jpg)
(http://www.dsboards.com/images/cast-3.jpg)(http://www.dsboards.com/images/cast-4.jpg)
But then, quite obviously some of the magazines worked with very outdated info - in the top cast list, for instance, Thayer David is listed as playing Matthew Morgan even though by the time the list was published, it had been two years since Matthew had been killed off and David had subsequently played Ben Stokes and was currently playing Prof. Stokes! ::)
As for the reasoning behind the name changes, I've never read why it was done - but Amy isn't the only example of a character being renamed after having already been referred to on the show as something else. For example, 1897's Edward was originally named Oscar, and in Ep #643 Roger discovers a letter Quentin had written to Jamison about Oscar.
The DS writers have said that they often chose names for the characters based on what the name's meaning conveyed about the character, either as a way to convey the character's essence or simply as a joke (as is the case with Angelique, who could hardly be considered angelic [lghy]). I have no idea what the meanings of Molly, Bob, Amy and Chris are - but if someone does, it might not only be interesting to know, but it could possibly give a clue as to why the names were changed...