James Miller, pretty much every source says, was Irish. He was an early settler back in the 1840s.
http://www.onlinebiographies.info/ca/marin/miller-j.htm .
That's the usual story associated with Mr. Miller. The one you dug up strikes me as motivated: He had to find a bad reason for the schoolhouse name and settled on a different James Miller to provide the required pedigree. They fess up to as much--their goal was to find a reason to change the name. Motivated thinking almost always produces the intended results "by any means necessary." Meanwhile, the usual story goes back quite a few decades and I'm not sure there's a compelling reason for anybody to misrepresent him as anything other than what he was, the son of an immigrant mixed up with Timothy Murphy who bought a land-grant before California became American territory. His presence and origins are well documented; the researchers have to show there are two distinct "James Millers" in the same area at the same time, and that the namer in question was the one that they've dug up for the first time. That's a tall order.
This says nothing, however, about any human trafficking that the probably unitary James Miller engaged in. Mr. Miller is, however, the source of the name Miller Creek, the surrounding school district is in, and what the activists would Dixie School District and the school itself named after. So if the activists you found are correct, those wanting the name change think naming the school after the South because it offends blacks is horrible, but want to name it, essentially, after somebody who enslaved Chinese and Indians. Quite a message they have, there. (I think both sides have been soaking their heads too long.)
As for "Dixie," the origin of this term itself is screwball. That's unlikely ever to be known. Whatever the origin, it was written as a parody, mocking the South. Since the song gave the name to the South, I go with "Dixieland" being in New York State, mostly because it makes the parody a bit stronger. Also can't quite sort out how a unit of currency from New Orleans would resonate so well with the Northern audiences the parody was intended for. Dixieland in NY State was eponymous, named after Mr. Dixie, the owner.
http://www.dixieschoolhouse.org/about-dixie-school-hosue.html says
Mrs. Frances Miller Leitz, granddaughter of James Miller stated that her grandfather not only donated the land but helped haul redwood from the Nicasio Mills for construction of both school buildings. Mrs. Leitz also uncovered the origin of the school’s name (“Dixie”) when she stated that her grandfather, no being a man to turn down a challenge, named the building “on a dare”. Marin County in 1864 was hotly pro-Northern and the fact that several Southern sympathizers helped in the construction of the first schoolhouse prompted someone to dare James Miller to name the school “Dixie”.
The only problem with that is the Dixie School District was formed in 1863 and wasn't named after the schoolhouse, according to other sources. Might just be that the schoolhouse was started at the same time the district was named, and both were named at the same time (or nearly so), but the schoolhouse wasn't finished until 1864. Still, it's a family story and there's likely some truth to it.
If so, it's not so much a tribute to the South as a sign that even then Marin County residents were willing to go against the tide of public opinion. (Whereas now, it seems, they want to go with public opinion.) Or that James Miller, at least, was easily goaded.
The superintendant's view, I guess it is, that it's named after a Me-Wuk Indian ...? Possible, I guess. Can't find any suggestion that this is the case, at least not online.
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