For example, your first quote is from Federalist 46. I'll put it in context:
"To these would be opposed a militia amounting to near half a million of citizens with arms in their hands, officered by men chosen from among themselves, fighting for their common liberties, and united and conducted by governments possessing their affections and confidence. It may well be doubted, whether a militia thus circumstanced could ever be conquered by such a proportion of regular troops. Those who are best acquainted with the last successful resistance of this country against the British arms, will be most inclined to deny the possibility of it. Besides the advantage of being armed, which the Americans possess over the people of almost every other nation, the existence of subordinate governments, to which the people are attached, and by which the militia officers are appointed, forms a barrier against the enterprises of ambition, more insurmountable than any which a simple government of any form can admit of."
No the militias that fought the british did NOT have officers appointed by the state. This was the type desired to be preserved.
“JUSTICE SCALIA: They {meaning the british - triple} certainly didn’t want to preserve the kind of militia that America had, which was a militia separate from the state, separate from the government, which enabled the revolt against the British.”