For a few moments, Daneel had no idea regarding what he should say.
Although this matter regarding Bartholomew had been in the back of his mind, he had been entirely absorbed in everything that he was mired in because of Jessica. Hence, this apology kind of came out of nowhere, and for a few seconds, he had to just keep looking into the Head's eyes while seeing the changes that were happening in them right after he had come out with the truth.
Where before there had been hesitation and self-doubt, there was clarity now, and this was the clarity that one could only achieve if they faced their inner demons and defeated them successfully, instead of sweeping them under the rug and resorting to things like excuses or justifications.