The whole question of what the pedal should play is very much open to individual interpretation - there's no autograph and the only two copies (Preller and Kittel, both quite a bit later than the date of composition suggested by the idiom of the piece) make no stipulation about what they play (although they are needed unless some chords are respaced in places). The earlier, shorter 729a is similarly unspecific (here the chorale is figured, not written out). The NBA has no pedal indication at all, the BG just (con Ped.), on who knows what authority. New Breitkopf suggests pedal for the first two chorale phrases, and then not until b39 to end. The 3-stave notation we're now familiar with is I suspect very much a development of the Novello editions. So a range of solutions is certainly acceptable. One possible system is just to use the pedal where you really need to, where the tune appears in fuller harmonised textures. Registration - possibly plenum, or a smaller chorus, but I've heard it done very beautifully on a single 8 principal.