Intelligent design derives from an early 19th-century explanation of the natural world given by an English clergyman, William Paley. Paley was the populariser of the famous watchmaker analogy. Proponents of intelligent design are crupping Paley's argument with a new gloss from molecular biology
In the last sentence, 'crupping new gloss' shows the word 'crupping' has been used to favor Paley's argument (as the term "proponents" is used), as with a gloss means making it look more attractive than it actually is. So destroying, testing and questioning are negative words in the context of the passage.