Are you sure he's taking a positive view of humans? I've found Miyazaki's movies to be anti-human in general.
(Nausicaa is a very strong example of what I'm talking about.)
Nothing Lady Eboshi does is wrong as far as I'm concerned, but that's because I don't like the environment as much as Miyazaki does. I think a certain amount of natural destruction is an acceptable trade for technological progress. But for Miyazaki, Eboshi becomes a useful antagonist because it allows him to examine the complexity of human relations with the environment; in other words, people who are fundamentally good may be causing a greater harm with human-centric actions.
I don't really see the contradiction that you describe between Eboshi and the samurai, because we're really talking about two different kinds of people.
Lady Eboshi is a fairly decent human being because she takes care of the social outcasts and gives them a sense of purpose the mainstream society (run by the samurai) denies to them. Further, the warring samurai are violent plunderers, so it makes sense there should be no rehabilitation for a bunch of sociopaths. As for why they are doing what they're doing, there's probably a specific historical context recognizable to a Japanese audience (I think the movie is supposed to be set in the Warring States period) but as a history buff I can say that in many wars armies simply degenerated into raping and plundering civilians to perpetuate the war, so since this is a time of war an attack on a town by even 'their own' allied army is highly likely.
I sense a double standard, but with less accuracy you're really doing the exact same thing as the movie itself is doing. No wonder you don't see it as a contradiction. If you did, then you probably wouldn't be doing it.
For example, you say that nothing Lady Eboshi does is wrong, but later describe her not as a perfect person, but as a fairly decent human being. The samurai aren't analyzed enough to determine if they are sociopaths, but regardless there's no realistic way they all could be. Some are probably psychopathic, and others probably have remorse though they follow orders, perhaps out of blind loyalty or perhaps out of fear. There could be fairly decent people among the samurai. You're judging them pretty superficially. I think the movie itself uses pretty much the same double standard you are using, so it's no surprise that you would too, but also it's pretty common for people to think the way you are.
I think your assumption about what Miyazaki's views are is wrong.
He's not saying all people are good, only certain people are.
That's why he's not going to waste cels and ink on rehabbing the soldiers.
If it was that important to him that all people be given that opportunity, he would have done so.
As I said before, I think that Miyazaki consistently takes a dim view of the value of humanity in relation to the environment, so that's already not consistent with a view of all human life as precious.
I have seen Nausicaa and it has pretty much the exact same portrayal of humanity, but a little more honest and realistic. But if you think my view on Miyazaki is that he's saying all people are good, then you have misunderstood what I said. To clarify, I believe that his view is that human beings are inherently good. In other words, we all have good in us, and we start out good but get corrupted as we get older. That's why he often strives to find the good in people, even greedy selfish people like Lady Eboshi. The samurai are portrayed as having been corrupted, not that they necessarily weren't good at some point earlier in their life. Again, not much is said about them because they just serve as an antagonistic force. He didn't go into depth exploring them, and that is the reason they don't portray any good in spite of his view that humans are inherently good. They're not being explored that way. They're simply a plot device.
Edit: Also I think he portrays the environment as vitally important as human life, hence the trauma of the god's death and the death and destruction that follow as a consequence. The people suffer as a result of destroying nature. Mononoke herself harshly criticises human beings for their destruction of nature, that is Miyazaki at least presenting the argument. I don't think he sought to portray either human life or nature as more important, but rather the balance necessary for both to exist.
I think you're right about balance, but the question is how much human life must be lost in the interests of 'balance'. I think that Miyzaki is writing from a posthuman perspective in Nausicaa that views the loss of individual human lives as acceptable in the interests of ecological balance compared to the more destructive humanism of Kushana, who wants to eradicate the poisonous trees to save human lives but damage the ecosystem in the process. To Miyazaki, it's not okay to damage that ecosystem even in the interest of saving human lives.
If Miyazaki will accept that position In Nausicaa, we can use it in Mononoke to explain why not all the humans need to be saved. The answer is that some people will end up not being as valuable as a plant.
They're not being explored that way. They're simply a plot device.
You're probably right about that, but since history at least provides insight into their motivations, at least that is covered. But I don' think it's necessarily a flaw because, as I've said, some humans are going to need to be expendable in Miyazaki's pursuit of ecological balance. For the satisfaction of the audience, it might as well be a bunch guys historically known for rapine than a modern humanist like Eboshi.
That's why I consider Miyazaki, at least on these topics, to be a misanthrope more than anything else.
He's definitely looking at the situation from a perspective beyond a mere human perspective. I think all great filmmakers do that.
that views the loss of individual human lives as acceptable in the interests of ecological balance compared to the more destructive humanism of Kushana, who wants to eradicate the poisonous trees to save human lives but damage the ecosystem in the process.
But this you've described here is not a posthuman perspective, it is merely a human perspective, and it is not what Miyazaki is getting at. The universe doesn't think in terms of what's acceptable and what's not. His posthuman perspective is trying to explore the relationship between humans and nature while analysing personality types. In the case of Nausicaa and Mononoke a lot of the same themes and personalities are there, but some of them are dealt with in different ways. I can't remember who said it, but, "A good movie presents two arguments well." Basically you have the hero presenting one argument up against the opposing argument of their adversary. The hero in both is confronted by a problem and sets out to discover what is causing the problem and solve it. The antagonistic forces do the opposite, they cause the problem and try to avoid dealing with it. They may pretend to deal with it in some manner, but ultimately they're lying about the real problem to avoid dealing with it. The posthuman perspective analyses these people and their arguments in various ways throughout the course of the film's events and tries to demonstrate the results of their actions through causality. Nausicaa was in my opinion more accurate. The people who destroy nature for their own personal gain without considering the consequences are evil. I think Mononoke tried to take it from the perspective that they're really good deep down, and I think Lady Eboshi's redemption was too forced and she wasn't criticised harshly enough.