But you must realize that the theory of evolution is a scientific theory. Any controversies, and there are many, are debated within a scientific context.
What ID, and creation "science" before it, seek to do is use belief, scripture and divine revelation as scientific evidence. They are not.
You say, "There are millions of people who believe that those holes can be explained best by something other than a lack of evidence." It doesn't matter what people believe about the theory of evolution. What matters is what the evidence says. And I have yet to see any science in creation "science" or in its younger cousin, ID. Rather, they are religious beliefs taking on the trappings of science in order to advance religious goals.
But The Origin of Species is exactly that - the origin of species. Darwin was not talking about the origin of life, he was observing how living things developed different physical appearances in response to environmental changes. Once he pointed it out, it was obvious.
It was never intended to explain the origin of life on earth, and it doesn’t. It doesn’t explain how lightning strikes or volcanic plumes might have reacted the right elements to form RNA precursors, and it doesn’t explain how those might become something that can have a cellular structure, find nutrients, and reproduce.
Instead, it’s just taken as dogma that this happened. Creation science was just silly. The Bible says it is to be taken on faith, so claiming that science proves it contradicts the nature of the Christianity. ID is another issue. The origin of life is unanswerable, at least to us, and the origin of the universe is unanswerable based on everything we know about physics.
It seems like this teacher is honestly appraising the situation and listing what we know and what we don’t know. Both sides have spent years saying we know it all and anyone who doesn’t agree with us is wrong. Good on him.