Besides, Jude Irwin was my father and he was good to me, and in a way, he was a man and I loved him. (10.450)
What Jack probably means by "in a way, he was a man," is that he can understand how the Judge's idea of suicide fit the Judge's idea of what it means to be a man. This is an idea, by the way, that the Judge has passed down to Jack. Because Jack can empathize with the act on some level, he is able to love the Judge in spite of it.