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If you say that you can't include God in science - I agree.
Then, as others have pointed out, you really DO accept MN. Your beef is not really with MN.
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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.
It sounds like your real concern is that by restricting science to MN, science may miss things. Not all truth will be accessible through science. I agree that this is the case, but I believe this is necessary for science to function (as you also imply in your first sentence above). As Erwin Schroedinger said:
I am very astonished that the scientific picture of the real world around me is very deficient. It gives us a lot of factual information, puts all of our experience in a magnificently consistent order, but it is ghastly silent about all and sundry that is really near to our heart, that really matters to us. It cannot tell us a word about red and blue, bitter and sweet, physical pain and physical delight; it knows nothing of beautiful and ugly, good or bad, God and eternity. Science sometimes pretends to answer questions in these domains, but the answers are very often so silly that we are not inclined to take them seriously.
Many types of truth are outside the realm of science, but this does not make them any less true. If we admit that science is limited in this way, there should be problem with restricting it to methodological naturalism. The advantage is that this makes scientific investigation metaphysically and religiously neutral; all of us can do science in a consistent way, whether Christian, Hindu, or atheist.
The problem is not with MN, but with the attempt by some (usually non-scientists) to broaden the definition of science to make all truth part of science. This can never be done in a way that we will all agree on.
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