Daru suffers from alienation because he must operate in an absurd world, a world that is irrational and meaningless, and his attempts to find some order in this world bring him into conflict, thus increasing his isolation. Within the setting of the Arab uprising against the French, Daru feels that his actions regarding the prisoner will make little difference, or they will be misconstrued anyway. Added to this, Daru is part of both cultures, so he operates with a certain ambiguity as to his loyalties.
No one in this desert, neither he nor his guest, mattered. And yet, outside this desert neither of them, Daru knew, could have really lived.
When the prisoner is brought to him by the "old Corsican," Balducci tells Daru that he will not denounce the schoolteacher if he does not comply with the military orders, so Daru must make his own decision. But, although the man's "stupid crime revolted him... to hand him over was contrary to honor." Thus, it is an existential decision that Daru must make in this absurd situation. Having to do this leaves Daru isolated because he follows only his own conscience and no rules made by either culture, French or Arab.