In earlier posts and comments, here and on prosblogion, Mike Almeida and I have been discussing problems with Molinism and stochastic processes.
Here's a way to put a variant of the problem (this may well duplicate some of Mike's ideas). Let C be the following set of circumstances: a fair indeterministic coin is tossed, with a machine set up so that if the coin landed heads, then laws of nature specify that the machine would cause all creatures in existence suffer excruciating and undeserved pain for eternity.
We can now do two different calculations. Let G be the claim that omnipotent, omniscient and perfectly good God necessarily exists. On the one hand, P(Heads|C)=1/2 (because the coin is fair). On the other hand, P(Heads|C and G) is less than 1/2. For such a God would be unlikely to allow C to be actualized unless he knew that the counterfactual C→tails is true. He might of course be planning to miraculously intervene after the machine activates, and so P(Heads|C and G) is non-zero but it seems to be part of divine providential goodness to avoid having to intervene miraculously, but surely P(Heads|C and G) is less than 1/2.
But now we actually have a contradiction. For the probabilities in question seem to be objective probabilities, and when we're talking of objective probabilities, P(G)=1, since G is a necessary truth. Hence, 1/2 > P(Heads|C and G)=P(Heads|C)=1/2. In other words, 1/2 > 1/2, which is absurd.
Therefore, we must reject one of the two probability claims. In particular, it seems, we need to reject P(Heads|C)=1/2. But this means that given theism, we cannot consider the probabilities that come from empirical study to be the genuine objective probabilities governing the events. Granted, in the case above, we were talking of a catastrophic case. But presumably even if the consequences of heads are somewhat bad, P(Heads|C and G) will still be somewhat less than 1/2.