The problem with the natural assumption is that it is the very same thing as the God of the gaps fallacy. That is - it is also fallacious.
God of the gaps looks at something we don't understand and says, "Goddit." Methodological naturalism looks at something we don't understand and says, "We don't understand that yet."
Where's the fallacy?
If you say that you can't include God in science - I agree. If you say you can continue to assess "truth" about nature - without God, I don't agree, because logically, you can now only come to a false conclusion, based on premisses which do not involve a Creator.
Of course, the beauty of science, and the flaw in your entire position, is that science isn't about assessing "truth" in nature. Thus, we can safely ignore the rest of what you say.
Moreover, science isn't based on the premise that there's no god. Thus, proving the falsity of that statement won't affect science in any way.
I should add that yes I am aware that pure science on a smaller scale, also logically assumes that God isn't necessarily involved. However - I will let you figure out the rest. Rest-assured, I have thought it all through, as per usual.
Well, since it doesn't appear that you've thought out what you did present, I'm not willing to give much credit to your assurance that you've thought the rest of it out.
Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them; and no man ever had a distinct idea of the trinity. It is the mere Abracadabra of the mountebanks calling themselves the priests of Jesus. -- Thomas Jefferson
For we know that our patchwork heritage is a strength, not a weakness. We are a nation of Christians and Muslims, Jews and Hindus -- and non-believers. -- Barack Obama
We see monsters where science shows us windmills. -- Phat