I have a take on the role of probabilistic arguments that might be of help here. Look, when it comes to the resurrection of Jesus, a person's decision to accept or not accept the Resurrection is likely to be a combination of the evidence specific to the Resurrection, and a prior assessment of how likely the background beliefs that are behind belief in the resurrection are to be true. We know that people who are thinking about the Resurrection are bound to differ about whether the claim that Jesus rose from the dead is antecedently plausible. There's going to be people who find the fact that something would have to be explained as a divine miracle grounds for giving it as close to a probability of zero as you can get. There are some people who are already committed to some form of supernaturalism, and who are not going to be deterred by the fact that the explanation involves the miraculous. So, how can we carry on the discussion? One way of doing it is to ask merely whether the evidence in more like what we should expect if the Resurrection happened, or whether it's more like what we should expect if it didn't. In other words, is there anything in the reports coming out of the first-century church that is more like what you should expect if Jesus was raised than if Jesus was not raised. If the answer to that question is yes, then the evidence confirms the resurrection, but it might still be rejected by reasonable people on the grounds that a Resurrection would commit you to the existence of God, or other features of Christianity that you consider to be improbable. Fine, but you can at least say, in response to the evidence, that the evidence directly bearing on the resurrection of Jesus is easier to explain if the Resurrection occurred than if it didn't. In other words, we can isolate one particular piece of evidence from the total evidence we have that bears on the issue and ask whether this piece of evidence supports the Christian claim that Jesus was resurrected or not.
Similarly, we can ask, concerning the fact of pain and suffering, how it impacts the credibility of theism. It could turn out that yes, pain and suffering adversely affects the credibility of theism, but it does not show that anyone who believes in the existence of God is just being delusional.
I understand that some people do Bayesian probability theory to get a correct final conclusion based upon agreed-upon methods for ascertaining probabilities. That's legitimate, but we also might like to isolate the impact of a piece of evidence on the overall plausibility of theism and Christianity. I find Bayes' theorem to be a helpful tool in doing that, even though I do not expect an agreed-upon conclusion concerning the Resurrection after we are done. To me, it's not a misuse of Bayes' theorem, just a different use.