I have taken the Family Magic Tour at Walt Disney World twice and both times we had Peter Pan as our "surprise" at the end. However, it is true that the character assignment is subject to change and it is quite possible that you will have another character as your special guest.
However, there is still plenty of opportunity for your daughter to get face time with Peter Pan. He is frequently seen in the parks. I have seen him in a variety of places over the
years, including on Main Street in the Magic
Kingdom and near the Peter Pan's Flight ride. His current guest
greeting area is just outside the Pirates of the Caribbean ride, where
you will also often see Hook and Smee too. When you enter the park,
pick up a free Times Guide, which will be located near the maps. This
should tell you when Peter Pan will be greeting guests at this
location. If for some reason this is not listed, just stop by the guest
relations office at any of the theme parks. Ask them to call the
"character hotline" for you and they will be able to tell you where and
when any specific character will be in the parks during your stay.
I also had a nice experience this past November with Peter Pan at the end of the Pirate
and Pals Fireworks Cruise I recently took with Moms Panelist Cathy and
her family. You can read Cathy's description of the cruise
HERE.
Hope you have a magical vacation!