I mean, you got one thing absolutely right: you don’t get it.
Firstly, Memoirs of a Geisha, book and movie, was orientalist trash, and has been called out as such, over and over again. Even someone as mainstream as Roger Ebert caught that, as cited here in an article very rightly noting that Hollywood is just fine with Asian women playing Asian women… as long as they’re prostitutes: http://www.rogerebert.com/far-flung-correspondents/memoirs-of-a-geisha-part-i-memoirs-of-postmodern-orientalism
Secondly, the problem with Hollywood substituting white actors for roles that were originally people of color is a problem of *America’s* representation of race, and the way the white American mainstream stereotypes minorities, marginalizes minorities, and disenfranchises minorities — and how the representation of minorities reinforces a white power structure that relies on and reinforces the marginalization of minorities, domestically, and in our foreign policy.
It doesn’t matter* that the Japanese are cool with it, or the original writer of GITS is cool with it. Those facts are totally irrelevant to the question of how a white American mainstream chooses to represent, or misrepresent, minorities. Our racism is OUR problem — we don’t get a free pass because some other country is like, “a-okay!” Because the whitewashing of POC roles serves to reinforce existing (racist) power structures, to reinforce bias, to represent America as a primarily white country where minorities are relegated to side roles at best, and where heroes must always be white. Pro-tip: heroes are not always white (just as all — or even most —crimes aren’t committed by black people, despite what 40 years of U.S. television might have led you to believe).
Our popular culture is one of the primary ways in which we learn about and understand the world (even if through a glass very very darkly). The marginalization of people of color in a dominant medium of popular culture matters very, very much. It reinforces and normalizes American racism: sometimes implicit, subtle, unconscious racism, but racism nonetheless.
Lastly, this is *very* far from a one-off — it’s a systemic, repeated, intrinsic pattern in how Hollywood deals with minority characters and actors. It’s easy to make some anecdotal argument about “well, THIS character is actually a cyborg!” and think that has some bearing on this issue, but it doesn’t, at all — because this instance is merely one among many, many, many, many, many. This is what Hollywood does, this is what white culture does, this is what white American power does: erase the meaning, the importance, and the very existence of people of color.