leaving all my thirst of blood in this aside, i can point a few things about your analysis.
if this teach anything is that if there is no 'judicial system' those in power will tend to be corrupt a lot more, and that makes the whole 'justice is for those that won and the loser are bandits' even more of a truth. be that the dark moon family, the lords or the ones trying the revolution: they are all working on washing their 'wishes' with blood so it can be turned into 'justice'. and to MC family they must be slaves, without factually being slaves, that is only the wishful thinking of the dark moon family and they can only turn this into reality if they are more powerful. in a world like that you can either submit or fight, you may try to hide but that wouldn't work with a whole clan. the whole topic of revenge remains a main topic in worlds that lack fairness.
about them being 'bad guys', there is not much to say about those that came to act the order from up above, we can see how asshole-ish they are. but if we focus on talking about the head of the dark moon family, i don't think it is as simple as him being 'bad', he is not killing only due to malice or for blind hate. he has no conscience tho, but in such world will anyone at the top have much of a conscience anyway? his move is actually smart, such a genius appear, he either kill him or let him grow until it can usurp his family position. the leader knows how much MC family suffered, so he knows no sweet words can gain much trust from them now that they have such powerful future leader, he knows that with such potential MC may achieve much more than he ever did... how can he let such seed grow? we can only say his decision is dumb, because he is up against a plot armored MC :P so he will fail or he will fail even harder. this whole thing is a good analogy for what happens with kings/emperors, they don't rise to the top, being nice and dandy... when it is only the strong that prevails, then there are always some that fail miserable, what is done to those that fail... in the eyes of those that lose, the winner are always 'bad' and in the eyes of those that win they themselves are always 'upright with justice'.
about the 'teaching children' i don't agree with you. the responsibility to teach children does not lie in some random media. those media (book/series/games/music/etc) represent only itself in some kind of context, those are not teachers. i do agree that such consumption of media should never be unsurprised, but the most important thing is to teach children how to read between the context! so that when they read about war, they can understand the conflict and consequences of such; if they read about porn, they can understand the difference between fetish and reality; if they read about super-powers, they can understand their analogies, the impossible and possible; if they read about science fiction, they can understand about progress, how hard it is, the complexity of society; if they read about history, they need to ponder who wrote it, how 'truthful' it is and how important it is and if there is anything they can by analogy learn about the present. see... it is not in the materials but in the people to be able to be conscious and actually think. those with power can always block a site or two they don't agree with, some media can always have some restriction to use, but there will always be more to each blocked, however if you teach them to think: problem solved (and actually this one and many others).
this whole thing with me not agreeing with your sentence, it is not that i would like manipulative media to order the world, i want such books to be available but someone must teach people how to really ponder and be conscious. an even more dangerous path is going with the 'don't think books should teach', because with that some would be censuring the many ways of society or the power of imagination and creativity, limiting our options to grow and learn, etc.
It's true that the dark moon family did a lot of bad thing and that even though those guys are just underlings they're pretty hateful too
But I don't really like the logic behind it, they're always like 'I must get revenge for everything did they to me' and ok, in this manga all the 'bad guys' are bad but in real life, oftenly not all of the bad guys are bad
I don't think books should teach children that 'tooth for a tooth, eye for an eye' kind of thinking
Well, i still like this manga but..