I don't think it would work even if somehow Bob was able to pull it off. After the Obi Wan/Anakin fight the rest of the film is a sombre montage, with a couple of small dialogue scenes mixed in - a Younglings massacre wouldn't fit tonally; plus, it makes no sense anyway: the Jedi are defeated, Palpatine is officially Emperor, why does Palpatine wait so long to attack the Temple?

I don't see what's wrong with the Clonetroopers attacking the Temple during the Order 66 portion of the film - after all, Clonetroopers are shown killing the Jedi, why not show them killing Younglings at the same time?