Jethro helps Eb in Chapter 9 because, when all is said and done, he would not be able to live with himself if he does not help someone who is so in need.
In his young life, Jethro "had never been faced with the responsibility of making a fearful decision like the one confronting him". He is completely aware of the consequences he and his family might have to face at the hands of the law if he helps Eb, who is a deserter. Also, he recognizes within himself a bit of resentment towards Eb, who has chosen to run while his brothers are sticking it out. On the other hand, he puts himself in Eb's shoes, wondering how he would react if he were as "sick and scared and hopeless" as he knows Eb is, and he considers that Eb has acted heroically for two long years, and that to ask him to do so indefinitely might be too much to ask. Mainly, though, Jethro wonders how it would feel to know that he was the one that sent his cousin to his death.
Jethro considers asking his Pa what he should do, but recognizes that his Pa would "be caught in the same trap (he's) in now...he'd put him in the spot where any way he decided would be bad - hurtful to a man's conscience". Jethro understands that his decision about whether or not to help Eb is one he has to make himself, and that there are no easy answers. In the end, like President Lincoln himself who grants amnesty to deserters like Eb who wish to return to their regiments, he makes his choice to the best of his ability after examining the situation from all sides, choosing to err, if he must, "on the side of mercy" (Chapter 9).