There is no such thing as someone who is "independent" and not "partisan." The federal bureaucracy is neither--it is comprised of people who, just like everyone else, are motivated by their own ideology and self-interest. Insulating those people from the elected President doesn't make them non-partisan. It just prevents the electorate from replacing those people with members of whichever party is currently favored.
You're correct that the founders were skeptical of direct democracy, but their solution to that was representative government and constitutional protections for private property. The people don't get to decide what to do, but they do get to decide who gets to decide what to do.
”Don’t let perfect be the end of good.” I would say it’s pretty common sense that avoiding an explicitly partisan situation would generally lead to less partisan outcomes.
You're correct that the founders were skeptical of direct democracy, but their solution to that was representative government and constitutional protections for private property. The people don't get to decide what to do, but they do get to decide who gets to decide what to do.