James Lindsay, the mathematician specializing on infinity has written a blog on how to define faith using Bayes Theorem. This is one of the coolest things on Bayes Theorem I have ever seen! The more I study this, the more sense Bayes makes. But this…..THIS is simply outstanding!
http://goddoesnt.blogspot.com/2012/12/defining-faith-via-bayesian-reasoning.html
God Is Odd: Exploring Theology(s) Dictums 
Bayes was also a prominent theologian, and believed in God in some way. It is highly unlikely that we would agree with the conclusions of those using his theorem to disprove God, as it were.
Why are you divorcing historical context from the application of the theorem? Bayes theorem makes sense to you, but Bayes himself would have vehemently disagreed with you? Isn’t that odd?