I think its true that by putting JW's side by side with Scientology, that Watchtower is always going to come off looking better by the comparison. Less nuts, less scary etc. So in that sense, they will come over as underwhelming.
On the other hand, by just making the connection between the two it inplants the idea that the JW are something scary and leverages the negative feelings that the audience have built up about Scientology over the course of the show and links them to JW's. Now, in people's minds, JW's don't go in the same box as harmless Christian religions, they belong in the box marked DANGER! LEAVE WELL ALONE. That is innoculation in my book.