I take anything at ENV with a grain of salt.
On the other hand, I do notice that when an ID paper manages to make it through peer review, some people over-react. We should just accept that peer review is an imperfect process, and get on with our lives.
Who says that the editors actually read the paper before publication? Better to blame the reviewers for acceptance. Still, one of the editors at least should have read the paper in conjunction with the reviews, and it should have been rejected.
I’m an author frequently published in peer reviewed journals, a frequent peer reviewer, member of the editorial boards of several journals and former editor of Research In Science Education.
This polemical piece in the OP includes a number of misconceptions about the role of journal editors in peer review.
The paper in question is not a scientific paper that reports new findings, it is essentially a review of the already well-known names and work in the field of intelligent design. I don’t have a strong view on whether or not it should have been published in this particular journal - that depends on the scope of the journal - but since so much of that work has been comprehensively debunked in the field of theoretical biology, I find the disclaimer unsurprising.
There is also a problem with the authors changing the keywords - or any other element - of a paper after it has completed peer review. It’s not a huge issue, and it’s not grounds for retracting the paper - and the journal didn’t. But it’s not good authorial practice.