If you listen to his final exchange with Elizabeth regarding the Hulk/John Doe it's very plain that his feelings have hardened a great deal after encountering Frye and his creature. She defended the other man (David) as a very kind, gentle man who wanted to cure himself and that McGee should leave him alone. Jack grimly responds "Ms. Collins, no matter how gentle this 'other man' may have seemed to you, the Hulk is a very real danger, and I will NOT leave him alone."