It was meant in an abstract way, regarding cultures, not individuals. To not be allowed to randomly kill anyone you want is the most basic rule of any social structure I know.
Honor killing is far from random and culturally enforced in many parts of the world, even today.
To a samurai, it is right to punish someone besmirching his honor, and given that honor can be placed above life, they naturally project their values onto everyone else(who doesn't?). Someone without honor is better off dead and it is Right by most of their moral standards(Honor offended equivalent physical injury, Social status placed above peasant as peasant is above animal, and on the practical level, retaining the fear and awe that keeps the ruling lord where he is(you'd find this is the key to all the old school rulers really, to retain power over the people, you have to wield the power)).
Remember, a (theoretical) samurai would totally not mind being killed for violating honor, especially if he hasn't got the guts to finish it himself for a greater offense.
A realistic samurai has to value his power and authority above the lives of others, or he'd be unable to retain said power and authority in a world where others can.
Actually, people tend to forget that Bushido as a code is incredibly strict and at times self-contradicting. In your example, an offense onto another samurai's honor would be met with a duel. However, said duel would need to be consented to by the respective lords of both samurai, and one would NOT be allowed to challenge the other without his lord's express permission. That said, the outcome of such a duel would also be willingly accepted by both parties as a just solution to the issue at hand, and no regrets are supposed to arise from the resolution itself. Quite rational when you stop to think about it, although some things can get to the realm of silliness (for example, it was considered poor form to pour sake with one hand to anyone but yourself, as that is the way traditionally employed to serve it in a funerary service; so if you served a lord with one hand, you'd be equating him to a corpse, meaning you either wish he were dead or he will be in relatively short time. Naturally, as people got drunker and drunker, decorum would be likely to fall and observance to such etiquette was likely to plummet - though most of the time they probably wouldn't care).
Let's also not forget that the Bushido itself is a creation of later eras - at the beginning of their existence the samurai class was little more than a bunch of glorified barbarians. Heck, they had
manuals describing the best way to sever heads so they would be easily recognizable upon return to camp for promotions.
All that said...
Cultural relativism MAY exist in D&D, but mechanically speaking, it doesn't.
In D&D, killing someone evil regardless of actions/etc. is a good act.
Killing someone good/neutral regardless of actions/etc. is an evil act.
Therefore the dread overlord Peckerus, who feeds on baby devils for breakfast and murders demons to the exclusion of everything else is mechanically good, even if he does so for no other reason than hatred or not wanting competition. Conversely, Dick the Champion of Kobolds, whom only murders paladins of a certain holy order dedicated to the extermination of pests in the world, and even so only when they are to kill a kobold, or in self-defense, is mechanically evil.
The potential for gray area morals in D&D certainly exists, but it has to be detached from the mechanics entirely, unless you want to rework the mechanics from the ground up.