Eizen wasn't expecting logic to get anywhere with the Ecclesiarch, but he tried regardless. He mustered his internal resolve and tried anyway. Maybe she, so unlike most of her brethren, had a small modicum of sense. Stupid Ecclessiarchy. At least Commissars wanted to kill you because you were dangerous, not for vague religious reasons. He felt that if the Emperor didn't want Psykers to exist, then they wouldn't exist anyway. It irritated him greatly that so many would so readily take the Emperor's judgement into their own hands. The hubris was disgusting.
Dohohohohoho
Vague religious reasons? Hating psykers is a fundamental part of the Imperial Creed, because they're a potential portal to the Warp that can explode into demons. It's in the rulebook, so to speak: purge the witch with blessed promethium is a tenant of Imperial faith. Religious persecution has good reasons rather than hurr durr them dumb fundies.
Hating psykers is good sense. There's a reason the Emperor had the Sisters of Silence.
I'm pretty sure his forbidden lore doesn't extend to knowing all this stuff. He knows about the warp, but not the SoS and so forth.
As far as he's concerned, he's being judged by a religious nutjob doing that judgement in
place of the Emperor whom it should rightfully belong to. Basically, he sees it as people claiming to have knowledge and wisdom on a level equal to Emperor. D'you get what I'm saying? (Not Tesera, you.)
Also, I find it quite hilarious that they're wearing the same necklaces. I wonder what she'd thought if she saw it. xD