It's possible that, at that point, Durkon genuinely didn't know Belkar is Evil, if he did decide "not to dwell on it" and depending on how seriously he took the "kill Elan for XP" incident and how much of the stuff Belkar said or did he heard or saw. It might sound far-fetched perhaps, but I don't see why Durkon would have encouraged Miko to scan the whole party otherwise, and I doubt Belkar would have told him about the lead sheet beforehand.