First, read this story.
This story raises up the tradition of keeping homerun balls and giving them back. As the article states, the first really famous situation of this was Marris's 61st where Roger wanted the fan to keep it. These situations always boil down to who is the nicer person. Is the fan going to say that I really respect your career and I am going to let you have your milestone back. Or, is the player going to say that I really respect your support, and realize that once that ball leaves the yard it is the fan's property, that I am giving literally to the fans.
While that debate could range on, it is clear, so clear, that the real problem here is the Phillies office skills. Most of the time when either the player doesn't step up (who in my opinion should always offer to) or if the fan doesn't step up, then the fan and the player start a barganing process for the ball. What the Phillies did here was wrong. They took the ball, told the girl she was going to get it back, and then gave her a different ball. Generally, when a fan gives up the ball, they get autographed balls, bats, pictures with the players and chance to meet them. This didn't happen here!
No matter how you feel about who did the right thing, it is safe to say that the Phillies PR department really botched this one.