while I obviously agree those are important ideas, a lot of our knowledge in "science" was done during times when this didn't apply, so I feel like free thought/equality is something that arises naturally as science marches on.
Other than the already mentioned experimental method, IMO the most efficient idea (which also would end up encouraging free thought) would be: "spread knowledge, build libraries, and don't burn books".
Perhaps simply the idea that knowledge could be transcribed onto physical objects and conveyed to other people across intervening time and distance would be a good candidate as the most important idea in human history?
Other than the already mentioned experimental method, IMO the most efficient idea (which also would end up encouraging free thought) would be: "spread knowledge, build libraries, and don't burn books".