Is it permissible to eat from food taken without right from provisions designated for the unit, and would it become permissible if taken with the intention that the person in charge of the kitchen had given it, and how can one be absolved of this?

The person in charge of nutrition is an honest trustee who is not permitted to act beyond what is authorized. Your refusal to take the orange was the correct action. Since you have completed your military service, you may seek God Almighty's forgiveness and give charity equivalent to its value.