I rather think that article writer is guilty of historical revisionism, particularly since she attempts to hang slavery on the Electoral College as though it were a primary intention rather than the fact that the elector numbers by state would have been by the same formula regardless of the 3/5 compromise.
The fact is that every state at that time considered itself an independent state. There was zero possibility that there could have been anything other than some kind of state-level vote for president--no state at the time was going to put its future into the hands of any other state. No state representative at the Constitutional Convention was going home with less federal power for his state than any other state had.
Therefore, all elections provided by the Constitution are state-level elections, including elections for the president: The states decide at the state level by state representatives who the state wants as president.