Is this finally what the quarrel's about -- "lawful cause-and-effect relationships?" Methodological naturalism is premised on Newton's laws, which basically describe the movement of bodies in space. But it seems there are things in the Universe -- such as consciousness, life -- that are immaterial, non-corporeal, and seemingly cannot be accounted for on the basis of Newton's laws. It seems MN puts such things outside the range of science. This does not make any sense to me at all. For it appears such things are quite "natural." IMHO FWIW
No. The overturning of Newton's laws didn't do a thing to methodological naturalism, which is the premise that laws exist to be discovered and what we see in nature can be analyzed in terms of whatever those laws are. Our current understanding of what the laws are is allowed to change if science is ever to get anywhere.
Science can do nothing without that premise and anything unreachable thereby is somehow not part of our world. The examples you give, consciousness and life, are inappropriate as they have long been under study by science.
I suppose if you start with the assumption that thigs can exist without a material embodiment -- yet magically interact with matter -- then not much of the world would make sense.