There are many reasons. First of all, Daru was born in a rural and economically poor area. He has sympathy for the Arab community. In addition, Daru does not want to commit himself to a "side" in the rising tension. With no declared war, no defined conflict, Daru does not feel it is morally proper for the French to be claiming jurisdiction in this case and he does not want to get involved.
This desire not to get involved - to not be forced to take on responsibility that is not his - is another reason that Daru resists. Consider this quote:
"I mean, that's not my job." "What! What's the meaning of that? In wartime people do all kinds of jobs."
"Then I'll wait for the declaration of war!"
To take on the additional responsibility is to take on the consequences of the action performed. Daru is not ready for that.
Finally, Daru is uncomfortable with the idea of the Arab as a criminal. Daru continues to ask "why?" and does not receive a satisfactory answer. Daru is looking for some reason to condemn the Arab. If the crime was inhumane, then the prisoner has sealed his own fate. However, if there was motive, it is possible that the prisoner will be unduly punished. Daru is uncomfortable with that because, again, by turning the Arab over Daru himself is accepting responsibility for the consequences. If the Arab is punished unfairly, Daru is in part responsible.