This isn’t anything major, just me re-listening to scene and realising stuff in hindsight.
On first listen, Elias’ reaction is solely stemming from his frustration with Martin and the burning of the statements. I imagine it wouldn’t have felt good, being as is it directly goes against all he, as an avatar of the Eye, stands for — destruction of knowledge and all that.
But, on second listen, his reaction is far more personal. Martin has unknowingly hit a bullseye with that statement, being as it was a letter to Jonah, and we have evidence of him being the sentimental sort, as with Barnabas’ bones. The little ‘oh’ is hard to hear, but it is there, and it’s definitely his reaction to the statement. The deep breath he takes after could, again, be frustration, but it could also be interpreted as him composing himself, preventing anything else from slipping through the cracks.