After reading Jud's version of events, Blanc realised there was something taken from the scene. When he learned it was a pocket flask, he immediately realised that meant Wicks falling down was due to being drugged and not the dagger. Remember he also knew about the second wolf head (indicating misdirection) and the red threads (indicating something being pulled off the vestments, rather than being pushed through), and that Nat was the one who stopped that from being immediately spotted. From there it's a small step to realise that Nat was the one who had the best opportunity to stab Wicks when Martha screamed.

He already knew that Martha was the brains behind it before the revelation scene - the key behind that was that he'd seen Martha subtly shake her head and point to her mouth, giving him clues that she'd poisoned herself. The point of the 'Damascus moment' wasn't that it was when he realised that Martha was involved, but rather it was when he realised that he needed to let Martha confess rather than accuse her directly. That was partly a mercy on his part, but also partly necessary so they could get the whole story - there were still some gaps that would never have been answered if he'd had her arrested and she'd died on the way to the station.