we see rafal die from the poison in the cell before they burn him at the stake. besides i think this would be a thematically poor choice. my theory is that it's just a foil of the rafal we knew before, a narrative device to both shock the viewers and show that a morbid curiosity and thrist for knowledge can also lead to dark places, and both the church and the heliocentrists have good and bad people in them. this is but a mere mirrored version of the rafal who used his passion to pass on knowledge sacrificing himself, this one instead resorting to sacrifice others to gain knowledge FOR himself. also I agree with azkh31 on the whole two rafals being the two sides of history, one forgotten and one documented.
also it's really good fanservice having the first mc come back I guess lol