For me having such thoughts doesn't relate to honesty but rather judging. It's not about being on someone's side or not - in general I think ideally the therapist should be on the side of the truth, whatever it is. However, having judging thoughts has not much to do with truth - it has rather something to do with therapist's countertransferential feelings.

The truth is more related to curiosity - why the person is feeling and behaving the way they do, what has led them to this situation - but to my mind this stance cannot exist simultaneously with judging someone's thoughts or feelings as wrong or thinking that they should get over them.