You say we have a long way to go before we base our lives on a completely rational basis.
While I am for being more reasonable about a number of issues, I don't think we will ever be completely rational. You only need to look at the human brain to see why this will never happen (so long as we remain something that can be called human).
We aren't completely rational creatures. We never will be. We are hard-wired for religious and other kinds of non-rational thought. These traits are there because they have helped the human race survive over time. While they are not all conducive to reason, they have been conducive to our survival thus far.
I don't know if a species that lived on a completely rational basis would be fit to survive. And I don't think a life lived by a human based on a completely rational basis would be worth living. I enjoy the nonsense in my life. You could argue that a completely rational life would take these factors into account and yada yada yada, but the kind of brain that would have reason tyrannize (even as a benevolent tyranny) like this would not be a brain apt to produce and enjoy various brands of nonsense in the first place.
Mr. Harris, I think, is asking humans to not be so human.
I would enjoy the product of a project designed to update religions and ethics, and I think it would be helpful, but the grand goal (like in the French Revolution) to have reason reign supreme is romantic nonsense. The Church of Reason is a farcical thing.