"It also disenfranchises voters, because ballots that do not include the two ultimate finalists are cast aside to manufacture a faux majority for the winner."
That's not how RCV works. The second choice is then included in the counts. No ballots are cast aside.
If I vote for A,b and c, and only D and E make it to the final round, my vote isnt counted in the final found. Often a voter is asked to rank their top 2 or 3, and many rank only 1.
That's not throwing away a ballot, any more than a person who voted for a person who lost had their ballot thrown away.
Ranked choice voting would likely undermine the two party system, and that is probably a bad thing. 3rd parties are generally more radical and less competent.