Definitions matter. "Methodological materialism" in your context changes to fit each new discovery, so discoveries like the Big Bang and the catastrophic formation of the Channeled Scablands which were derided in scientific circles because of their tangential support of Biblical accounts don't satisfy your question. But at the time, they did indeed require abandoning what were considered at the time to be "methodological materialism" for a seemingly religious explanation. After which, the definition of methodological naturalism expanded to account for each.
In which of your examples was "methodological naturalism" expanded to include an intelligent designer or the direct hand of the Creator?
Well yes, science is cumulative, and the theories about specific historical events have to be adjusted to fit new evidence. So far the adjustments haven’t required believing the earth is flat or that the sun revolves around it, or that it is 6000 years old.
And yes, scientists tried to fit geological findings into a Biblical framework until about 1830, at which point most admitted that a different interpretation was required.