In Bayesian terms, what is the rationale behind this having a lower prior probability?
This is incorrect. The prior probability represents your state of knowledge before seeing the evidence, not afterwards. In Bayesian terms, the reason "a theory [hypothesis] that explains only one or a few data points is less likely to be true" is because of the likelihood, which measures how well the hypothesis explains the data points, not the prior.
I'm going to avoid examples based on deities or psychic abilities as they just play on cognitive biases and get in the way of thinking clearly about the reasoning. So lets choose a less contentious example instead. Assume we have only two mutually exclusive and exhaustive hypotheses: H1 the coin has two heads, and H0, the coin is fair and has a head on one face and a tail on the other.
We start by stating our prior belief. Being objectivist Bayesian for this sort of problem, I am going to assume that I have no prior knowledge which hypothesis is more likely to be true, so I will assign a uniform prior distribution p(H1) = p(H2) = 1/2.
We then need to determine the likelihood for each function, which is the conditional probability of observing the data under a specific hypothesis. Let X represent the number of heads, then for a single coin toss under H1 we have p(X=1|H1) = 1 and p(X=0|H1) = 0, and under H0 we have p(X=1|H0) = p(X=0|H0) = 1/2.
So lets assume that we have a witnessed a single head, then we can work out the posterior probability of each hypothesis using Bayes rule:
P(H1|X=1) = P(X=1|H1)P(H1)/P(X=1)
= P(X=1|H1)P(H1)/[P(X=1|H1)P(H1) + P(X=1|H0)P(H0)]
= 1*0.5/[1*0.5 + 0.5*0.5]
= 2/3
and similarly:
P(H0|X=1) = P(X=1|H0)P(H0)/P(X=1)
= P(X=1|H0)P(H0)/[P(X=1|H1)P(H1) + P(X=1|H0)P(H0)]
= 0.5*0.5/[1*0.5 + 0.5*0.5]
= 1/3
So H1 (two-headed coin) has a higher posterior probability because it "explains" the observations with a higher likelihood.
Now if coin tosses are independent (the probability of one coin flip doesn't depend on any other flip of the coin) then we can Use our posterior probability after the first coin flip as our prior belief for the second coin flip and apply Bayes rule again to update our state of knowledge after the second flip (which is also a head). So now P(H1) = 2/3 and P(H0) = 1/3,
P(H1|X=1) = P(X=1|H1)P(H1)/P(X=1)
= P(X=1|H1)P(H1)/[P(X=1|H1)P(H1) + P(X=1|H0)P(H0)]
= (1*2/3)/[1*2/3 + 0.5*1/3]
= 4/5
and similarly:
P(H0|X=1) = P(X=1|H0)P(H0)/P(X=1)
= P(X=1|H0)P(H0)/[P(X=1|H1)P(H1) + P(X=1|H0)P(H0)]
= (1/2*1/3)/[1*2/3 + 1/2*1/3]
= 1/5
So you can see that as we add more datapoints, our posterior belief in H1 grows (as long as they are all heads), but it is nothing to do with the priors, it is because of the likelihood. The more data we have, the more the likelihood can change our state of knowledge.
So returning to God, what an objectivist Bayesian would do is to assume that a-priori the existence of God (H1) is equally likely as the non-existence of God (H1) and say P(H1) = P(H2) = 0, or adopt a hyper-prior, which we have gone over on another (but not very different) question.
The difficulty is then how to specify the likelihood of the evidence (e.g. testimony of prayers being answered or not answered) under both hypotheses. I suspect that will be the sticking point as your view on how the likelihood should be constructed will be different for different people, and you will have to make do with a subjectivist Bayesian analysis. In that case different people may come to different conclusions, but at least both will have explicitly stated their assumptions in a quantifiable manner which makes them more open to testing than if they just stated their opinion in natural language. That is the benefit of subjectivist Bayesian reasoning - it is demonstrably rational (c.f. Cox axioms) and it stops people from hiding behind the ambiguity of natural language (for some that is probably a bug rather than a feature).
I really would recommend reading an introductory book or tutorial on Bayesian analysis before asking more questions about it, it would be a much more efficient approach.