The court's five conservatives agreed with Alabama officials that Domineque Ray could be put to death without an imam present in the execution chamber, even though a Christian chaplain who works for the prison system is in place for other executions.
The court's short order did not deal with the religious issue, saying only that Ray made his request too late. His lawyers, and the court's liberal members, disputed that.
The blowback was immediate.
"I can't recall the last time that I was as shocked by a Supreme Court decision," said Deepak Gupta, a Washington lawyer who argues before the justices. "This decision is indefensible on the merits, and the court doesn't even bother to try."
Amir Ali, Supreme Court and appellate counsel at the MacArthur Justice Center and a lecturer at Harvard Law School, said the court's order was in contrast with recent decisions that have protected religious rights.
"Consider the opposite circumstance - a Christian person who is told that, during the final moments of his life, he can have only the services of an Imam," Ali wrote in an email. "It is hard to imagine the court reaching the same result as it did here. And that's a real problem because the very purpose of the Establishment Clause is to prevent this sort of religious preference."
Criticism from the right was strong, as well.
"The Supreme Court Upholds a Grave Violation of the First Amendment," was the headline above conservative commentator David French's article in the National Review.
"Any policy that by law or practice provided death-row inmates with access only to Christian chaplains would likely fail 9-0 if addressed on the merits," French wrote. "In this case, however, the Supreme Court didn't decide the merits. It determined that Ray's request for an imam was made too late."
The five justices who allowed the Alabama execution to proceed - Chief Justice John Roberts and Justices Clarence Thomas, Samuel Alito, Neil Gorsuch and Brett Kavanaugh - lifted a stay imposed unanimously by a panel of the U.S. Court of Appeals for the 11th Circuit.
That court said Ray had raised a "powerful" argument that prison protocol favored one religion over another: "it looks substantially likely to us that Alabama has run afoul of the Establishment Clause of the First Amendment."
It called for additional briefing in the case, but called for quick resolution to keep Ray's execution on track.
Instead, Alabama filed an emergency request to the Supreme Court, saying it should be allowed to go ahead with the procedure it had put in place to conduct executions in an "orderly and secure fashion." That meant having only correctional officials, which included the prison chaplain but not the imam who had been attending Ray, in the death chamber.
The Supreme Court majority did not address the religion issue, noting only that Ray - on death row since 1999 for the rape and murder of a 15-year-old girl - learned of his execution date in November, and waited until January to file a lawsuit challenging the exclusion of an imam.
In a dissent that called the majority's decision "profoundly wrong," Justice Elena Kagan said there was a reason for that.
The relevant Alabama statute, she wrote, provides that "both the chaplain of the prison and the inmate's spiritual adviser of choice 'may be present at an execution.' " Ray learned only days before filing the suit that prison policy meant his imam was not allowed to be in the room at the time of his death.
Kagan said there was no reason for her colleagues not to allow the lower court to examine the issues surrounding Ray's case.
"Ray has put forward a powerful claim that his religious rights will be violated at the moment the state puts him to death," she wrote, joined by Justices Ruth Bader Ginsburg, Stephen Breyer and Sonia Sotomayor.
"The Eleventh Circuit wanted to hear that claim in full. Instead, this court short-circuits that ordinary process - and itself rejects the claim with little briefing and no argument - just so the state can meet its preferred execution date."
Because the court did not address the religious issues in the case, it creates no precedent for similar cases in the future.
The absence of such acknowledgment struck some as a sign the court is more alert to discrimination against Christians than other religions. The court's conservatives, for instance, allowed Christian business owners with religious objections in a separate case to opt out of federal regulations requiring contraceptives be part of insurance coverage.
"Next time the court claims that religious liberty justifies casting aside some other important principle, like nondiscrimination on the basis of sexual orientation or women's rights, we should remember what the court did here," said Gupta.
Some who disagreed with the decision say they do not believe anti-Muslim bias was the cause of the order, but the court did itself no favor by not addressing it.
Ilya Somin, a conservative professor at the Antonin Scalia Law School at George Mason University, posted on the Volohk Conspiracy website that the decision was a "grave injustice," but likely motivated by the justices' impatience with last-minute death penalty appeals.
But "to say that this factor likely explains the ruling is not to say that it excuses it," Somin wrote. "The fact that activist lawyers sometimes abuse the process does not relieve the justices of their obligation to carefully consider the facts of each case on their own merits."
The court has ruled in favor of Muslims who have been discriminated against because of their clothing, and in favor of a Muslim prisoner who had to sue prison officials for the right to grow a beard for religious reasons.
But Ali said the court's 5-to-4 approval last term of President Donald Trump's ban on travel for some from Muslim-majority countries stung Muslim lawyers. He pointed to language in Roberts' majority opinion.
"The court went the extra step of saying that there was 'persuasive evidence' for banning people from several majority-Muslim countries," Ali said.
"If that was a gut punch to the Muslim community, this will be seen as a follow-up kidney shot."