The movie's philosophy was illogical
The first half of the film makes such an effective and intimate argument for the beauty and power of sex between a husband and wife, that it undermines that second half of the film. If von Trier really believes in the spirituality of lovemaking, how can he find Jan's salvation through Bess sexually debasing herself? The idea might have been plausible if Jan asked her to find another man who she could truly love, so that he would know that she was actually "making love" and not being systematically and willfully raped, but this is not the case. As it stands, his request is perverse, cruel, and twisted.
But because von Trier is determined to make Bess into a Christ figure, he has to make her suffer for her love. What destroys the analogy is that mankind did not ask Christ to suffer for mankind. Christianity is based on the notion that God offered Jesus to suffer and die for us, not for God. In "Breaking the Waves," Jan asks Bess to suffer for him, and she does, for him. Therefore, she is simply fulfilling his selfish desires, thus diminishing his ultimate redemption. If God had asked Bess to suffer in order to save Jan, the analogy would have been more complete.