The argument was him basically saying something equivalent to "If I had a disease that had a 1 in a million chance of survival and I survived it, it's not because I was the 1 in a million, it's because it was due to god's intervention". So I tried to point out that either his (subjective) base rate is wrong or his (subjective) conditional probability is wrong.

There no reason why God in principle should be unable to choose which of the people of the mass of one million survives. If you don't have a model of how the one in a million gets cured you don't know that it wasn't the God of the gaps.

In medicine you do find some people having theories according to which nobody should recover from cancer. The fact that there are cases in which the human immune system manages to kick out cancer does suggest that the orthodox view according to which cancer develops when a single cell mutates and the immune system has no way to kill mutated cells is wrong.

Today we have sessions with a psychologists as the standard of care for cancer patients and we pushed back breast cancer detection screening because a lot of the "cancers" that the screening found just disappear on their own and it doesn't make sense to operate them away.