I think what Harry was doing was trying to impress on Charity the need to make a clean breast. Thinking of the immediate issue, she might have been right that Molly could get away with it, but that was not viable in the long-term. For a mother facing the possibility of her daughter's execution is much worse than a nebulous danger down the road, that she cannot really grasp, being warned of by a man she reflexively mistrusts especially where her loved ones' safety is concerned. No matter how certain Molly's fall to darkness might have been if they hid her from the Council, that is a problem for tomorrow, and infinitely preferable to the suggestion that she surrender her daughter for a capital trial today.
For someone with a more objective viewpoint, however, Molly needed to stand trial. Having already started down the path of black magic, and attracted the attention of powerful dark entities of the Nevernever, the only hope she had was staying on the straight and narrow. She needed the supervision of a proper wizard with the strength and proper magical training to protect her from her own worst impulses until she gained enough control and maturity to sink or swim on her own. An underground apprenticeship and attempt to stay off the Council's radar would almost certainly lead her to full blown warlock-hood, and even if it did not, as she grew in power and ability she would eventually come to their attention one way or another and in such a circumstance, even the scant mercy she did receive would never have been offered. Look at the career of Elaine as an example: she did not have Molly's taint, and was forced to take refuge with the faeries and induced to assist in a plot to drasticaly upset the balance of power in the supernatural world. Even Harry himself had to turn to the Leanansidhe to survive Justin's attempt to exploit him, and does not seem all that sanguine about his chances of survival without the sponsorship and tutelage of Ebenezer. Even if Molly never again violated one of the Laws, and still managed to evade the notice of the Council, how long before something worse tried to exploit her as Justin, Lea and Aurora took advantage to attempted to take advantage of Harry & Elaine?

Note too, that Forthill, whose obligations as a priest were first to the Carpenters, no matter how highly he might think of Harry (and he would almost certainly pick Michael over Harry every time anyway), supported Harry's position despite his presumptive lack of knowledge about the Council and their inner workings. That almost certainly means that he felt it was the best choice for Molly's moral and spiritual well-being, regardless of the issues of getting away with it or not.

While Harry's statement might have been factually incorrect about the immediate disposition of Molly's offenses, for all intents and purposes, he was right that she could not get away with it forever, and would certainly face a fate as bad or worse than what she might get from the Council if she surrendered at that point.