Food dye to simulate stained glass
The lollipops are the glass, so you couldn't substitute food dye alone. The sugar in them provides the bulk, and nothing else is comparably transparent. You'd either get dyed pancake (painting rather than stained glass) or just a stain on the pan. You could substitute home-made coloured sugar/hard candy, for which you'd need any (water-soluble, i.e. common) food dye.  But this would be a lot of work to make several colours so buying lollipops or some other boiled sweets/hard candy would make more sense unless you specifically wanted unflavoured glass.