I would say yes - after all pepsin is a digestive enzyme. I'd venture to guess that it is probably optimal - since the body will focus its energy into cleansing the mucouid plaque that would otherwise be used for digesting regular meals.
What I like about Dr. Kelley's advise is the sensible nature of it. ie: if you feel sick: stop it or cut back. I would try it and if it does not feel right then hold off until you break your fast.
That said: clearly I am simply making deductions here. Perhaps someone else can pipe in?