Science is a methodology for studying the universe and everything in it, as well as the conclusions reached over time from repeated use of that methodology. That’s all it has ever been and ever should be.
The traditional view of God is of a Creator of the universe. He is not a part of the universe, otherwise he could not have been its Creator, therefore science can never study him. And what science cannot study, it has no business making judgements on.
That religion has wrongfully intruded on scientific matters with ancient creation myths means that science CAN rightfully debunk those myths. It does not follow, however, that Theism itself has been disproven by science, because science cannot do that. It can only show what dogmas in religion that relate to things in the universe are wrong, but not dogmas about anything outside the universe!
And that is why P Z Myers’ assertion here that “if you’re not an Atheist, you aren’t doing science right” is really a case of arrogant dogmatism on his part and need not be taken seriously by anyone who knows what the real conception of God by most theistic religions is.