Daru is told by Balducci that the Head officer could not spare him long enough to escort the Arab prisoner all the way to the French authorities. Balducci tels Daru it will be up to him to complete the transfer of the prisoner. Daru does not want to do this because he doesn't feel it is his job. Daru also does not wish to take sides against the Albanians until he has to choose to fight for France. Daru doesn't want to be involved in this messy business.
A good reason for Daru to do as he is asked is that the French government is expecting him to follow their orders. He is being handed a responsibility and should fulfill that responsibility even if it is an unpleasant thought. His refusal could look like a betrayal to the French.
just a clarification, its algerian not albanian :)