This will be a matter of interpretation.  I think that Achebe feels that Jonathan did the right thing by giving the money.  Achebe's focus is on Jonathan's work ethic and his willingness to rebuild his life.  Jonathan is shown as someone whose commitment to work and willingness to do what must be done represents the essence of his success.  In a post- civil war setting, Achebe makes the argument that nations can rebuild and societies can triumph over hardship and destruction if they possess the will and drive of someone like Jonathan.  It is for this reason that Achebe feels that he did the right thing by giving up the money.  Achebe's hopes of establishing a "civil peace" rest with the progressive attitude that Jonathan displays at the end of the story:

I count it as nothing...What is egg-rasher? Did I depend on it last week? Or is it greater than other things that went with the war? I say, let egg-rasher perish in the flames! Let it go where everything else has gone. Nothing puzzles God.

Jonathan is focused on prosperity and peace and is not shown to be resentful or self- indulgent in his anger. The fact that he is hard at work the next day, seeking to provide for his family, who have followed his example in how they work represents that Achebe believes that Jonathan did the right thing in giving the money to the thieves and focusing on the larger mission at hand.  For while the money has gone "where everything else has gone," Jonathan's work ethic still remains and because of this, Achebe feels that Jonathan and others like him will find success in a world where "civil peace" can prove to be elusive.