Iguro Obanai might have stopped pressing Tanjirou, who has broken bones and injuries all over the place, on the rock ground, but he still told Sanemi to bring Nezuko into the dark area. He is still enabling Sanemi instead of telling him to stop or staying quiet, so he didn't completely stop.
Except that the Master is the one saying to let them be. They may not trust Tanjirou and Nezuko, but to not trust, or in this case, have no faith in the judgement of the Master is a major issue.