There are a few things you can do:
1) Explain why Fully General Counterarguments are bad.
2) Explain why this particular counterargument doesn't make sense. This comment by pragmatist puts it nicely:
A consequence of ["God works in mysterious ways"] seems to be that the distribution over possible world states, given the hypothesis that god created the world, should be close to maximum entropy. This means no observation of the world state could count as much evidence for the hypothesis.
Alert: inferential distance failure!
You would have to make them first read the sequences and learn university-level math and physics. And probably some philosophy of science.
These are written from the angle that Christians deconverting is bad.
Cognitive reasons
Breaking up because a relationship with God becomes unworkable
Leaving because other Christians aren't empathetic about doubt
At what age do people leave?
It looks as though there may be more articles in the series.