The Alabama order comes as the U.S. Supreme Court heads toward a potentially historic, nationwide ruling on the divisive social issue. Last month, the high court announced it would hear arguments on whether gay couples have a right to marry everywhere in America, and a decision is expected by late June.
Thomas criticized his fellow justices for looking "the other way as yet another federal district judge casts aside state laws," rather than following the customary course of leaving those laws in place until the court answers an important constitutional question.
"This acquiescence may well be seen as a signal of the court's intended resolution of that question," Thomas wrote in an opinion that was joined by Justice Antonin Scalia. "This is not the proper way" for the court to carry out its role under the Constitution, he wrote, "and, it is indecorous for this court to pretend that it is."
The opinion was remarkable less for the legal result it suggested than for its open criticism of fellow justices.
After all, many legal commentators have predicted not only the case's outcome this spring (in favor of same-sex marriage), but the vote (5-4) and the author of the majority opinion (Justice Anthony Kennedy).
The number of states in which gay and lesbian couples can marry has nearly doubled since October, from 19 to 37, largely as a result of terse Supreme Court orders that allowed lower court rulings to become final and rejected state efforts to keep marriage bans in place pending appeals.
Alabama became the 37th state in which same-sex couples can marry, following U.S. District Judge Callie Granade's ruling in January that struck down as unconstitutional the state's statutory and constitutional bans.
Granade had put her order on hold until Monday to let the state prepare for the change, and State Attorney General Luther Strange had asked for the delay to be extended for at least a few months.
But when Monday morning came, probate judges in Alabama began issuing marriage licenses to same-sex couples, some of whom had been lined up for hours.
The Supreme Court often freezes lawsuits in place when they raise the same issue the court already has agreed to decide. And when federal courts declare state laws unconstitutional, "our ordinary practice," Thomas wrote, is to prevent those rulings from taking effect while they are being appealed.
But since October, the justices have repeatedly turned away state requests to keep same-sex marriages from taking place until appeals are resolved.
Alabama's plea was the first since the court stepped into the issue last month to take up a decision by the 6th U.S. Circuit Court of Appeals to uphold laws in Kentucky, Michigan, Ohio and Tennessee that define marriage as the union of a man and a woman.