Is designing a program for letters of guarantee and documentary credits for a contracting company considered a sin, and what is the legitimate legal arbiter for designing programs that may involve both the unlawful and the lawful?

As for letters of guarantee and letters of credit, there are permissible and prohibited types. If you know that the contracting company operates in permissible activities, then it is permissible for you to design the program; otherwise, it is not. The basic principle regarding program design is permissibility, but it is forbidden to design a program if it is known that it will be used for something prohibited, because that constitutes aiding in sin.