Gill told Rolling Stone magazine that he now aimed to "punish the wicked."
"In other words, to punish those who oppose the LGBT cultural agenda," added Archbishop Chaput, saying that conflicts over sexual freedom and identity involve "an almost perfect inversion of what we once meant by right and wrong."
The archbishop said Catholics must treat all persons with charity and justice, including "those who hate what we believe."
"It demands a conversion of heart. It demands patience, courage and humility. We need to shed any self-righteousness. But charity and justice can't be severed from truth," he said, citing St. Paul's Letter to the Romans and other biblical calls to "sexual integrity and virtuous conduct."
For the archbishop, attempting to soften or detour around these calls would demean what Christians have always believed and "reduces us to useful tools of those who would smother the faith that so many other Christians have suffered, and are now suffering, to fully witness."
Archbishop Chaput suggested that the article got points of American religion incorrect. American Baptists, for instance, see their faith as undermining the integration of Church and State.
"Foreign observers who want to criticize the United States and its religious landscape – and yes, there's always plenty to criticize – should note that fact. It's rather basic," he said.
The archbishop praised religious liberty legal groups like Alliance Defending Freedom and Becket, saying they are "heroes, not 'haters'."
"And if their efforts draw Catholics, evangelicals and other people of good will together in common cause, we should thank God for the unity it brings."
His column said the La Civilta Cattolica article was "rightly criticized" and "unfortunate comments," voicing a broader warning against misunderstanding the political and religious situation.