Destro has a code of honor. So do some organized crime families. Doesn't necessarily make them good people. A "code of honor" doesn't equal "good". During World War 2, the Japanese had a code of honor and disrespected those who did not share that code (such as enemies who surrendered).

Sunbow GI JOE writers guide called Destro a logic evil. They considered Cobra Commander as chaotic evil (crazy). Destro is rational, logical, a proper "gentleman" (more so in the comics) and still involved with evil. So he could be considered worse than Cobra Commander. Cobra Commander is inherently psycho, probably rotten to his core. Destro made a choice to be evil.