I'm newly registered, so apologies for what seems like a delayed reply.
There is a similar issue in the first movement of the Symphonie-Passion. Top pedal F sharps starting at bar 16 of the Jesu Redemptor section. One way round this is to take the F sharps with the right hand on the swell, which is coupled to pedal at that point anyway.
This is easier and doesn't seem to affect the music in any way.
EC