My DD (age 7) and I did the FMT back in December and had a great time.
As the above poster mentioned, the tour isn't really impacted by how busy the MK is. You just go about your tour with the tour guide regardless of the rest of the people at the MK.
I thought the pace was very leisurly. Given that we were on the tour during a very slow time of year (Monday, Dec 13 to be exact), there was only one other family on the tour with us. They had a boy about 4 and the pace seemed fine for him. You do cover most of the MK in the 2 hours but again, pace seemed leisurely and there were periodic stops to look for 'clues'.
We did the tour on our last day which I really liked because we had 'done' the MK very thoroughly on other days so we were very relaxed and not worried about 'missing' ride time. I think it just depends on your mindset. On one hand, doing it first thing would be a great way to kick of your vacation and get the 'lay of the land' so to speak.
Happy planning! I would highly recommend the tour.