Is this Guybrush character actually making fun of science and dissing the scientific method while using computer technology invented by applying the scientific method
? Yes, yes he is. He was not the first to do this, and he will not be the last. Sigh.
The scientific method has nothing to do with atheism or religious belief. Chemistry and biology experiments don't vary depending on the religion or lack thereof of the people doing the experiments. Science will consistently give the same answer no matter what you believe in.
This the point in the discussion where I bring up the obvious point that science is about what works in application, not what people wish or hope would work. Religions based on invisible supernatural beings have to make all kinds of excuses for their gods, because their stuff does not work.
Let me say it again: if religions worked as people say they do, we would never have needed science. We would have just prayed to whatever god, god would fix the problem or not, and that would have been that. Of course, for many thousands of years, that is exactly what people were stuck doing. The past ten thousand years have been a controlled study of applying belief in religion to human problems like the earthquakes and volcanoes, how to communicate and travel reliably and quickly, how to cure leprosy and smallpox, what causes mental illness. And the problems stubbornly remained incomprehensible.
Until we figured out a way to systematically figure out what worked, what didn't, and to separate the two. We figured out what made sense, what reflected reality and what didn't. Now we know what causes earthquakes and we can build to account for them; we can tell when different kinds volcanoes will erupt and evacuate people.
After we stopped begging the invisible gods to save our babies from smallpox and started vaccinating them--haven't heard much about smallpox recently have you? Instead of praying to gods to keep from getting cholera and typhoid, we wash our hands and devise sewer systems that keep the water clean. Amazing how many fewer people die of these things in places that apply science, compared to how many die in places where people are still depending on the whim of the invisible gods.
Now that religion has show itself to be utterly worthless in explaining everyday illnesses and natural hazards, the religious folks have retreated to the questions that scientists can't yet answer: theoretical physics and the origins of the universe. Because believing in gods always gave the correct answers before--why would anyone think that those stupid scientists will figure out the other things we don't yet know?