Lewis is saying that if you've disproved faith, your reason is flawed. After all, faith must be right!

This is 'extraordinary claims require extraordinary evidence', but in unfamiliar garb. We're not used to seeing it used the other way. (If a study reports ESP, then we ought to suspect problems in how it was conducted or analyzed rather than accept its conclusion - to use a recent example.)

I'm sure there are a number of relevant LW posts on the topic like "Einstein's Arrogance".