The Supreme Court, on the day before Justice Anthony Kennedy announced his retirement, upheld President Trump’s ban on travel to the United States from seven countries, five of them overwhelmingly Muslim. In Trump v. Hawaii, the court majority refused to consider the president’s statements of anti-Muslim hostility that led up to the ban—as a presidential candidate, he had said “I think Islam hates us” and called for “a total and complete shutdown” of Muslims entering the country.

But earlier this month, the court decided in the Masterpiece Cakeshop case that a civil rights commission’s order that a baker serve same-sex weddings was invalidated by the statements of two commissioners displaying hostility toward the baker’s religious belief in traditional marriage.

It is unfair to accuse the court majority of hypocrisy in these two cases, as some have done. But the majority did miss an important opportunity to give teeth to one of the nation’s most basic constitutional principles: the prohibition on official religious bigotry. I filed or joined briefs in support of the religious liberty claims in both cases, regarding the travel ban and the cakeshop, and wish the court had protected both.

The majority did miss an important opportunity to give teeth to one of the nation’s most basic constitutional principles: the prohibition on official religious bigotry.

The majority in the travel ban case held that Mr. Trump’s statements were irrelevant because under previous cases governing immigration policies, courts do not look behind the terms of a policy that is facially (or “on its face”) neutral (in this case, facially religion-neutral). And it is easy enough to distinguish Trump v. Hawaii from Masterpiece Cakeshop v. Colorado Civil Rights Commission on this ground: Courts give great deference to the executive branch in the context of immigration and national security. Moreover, the context of Masterpiece involved statements by commissioners acting as adjudicators; we have a special concern that judges deciding an individual’s case should not give even the appearance of partiality.

But as constitutional scholar Ira Lupu once said, every religious freedom case has a context. The travel ban was also distinguishable because Mr. Trump’s statements were even more clearly indicative of the decision-maker’s motivation than the statements in the Masterpiece case: He alone was the ultimate decision-maker. Moreover, his statements were especially unambiguous in their attack on all people of a religion merely for their membership in it. The Masterpiece statements were quite bad, but Mr. Trump’s were worse.

The court should not have focused solely on the travel ban’s terms, which it said did not show a clear pattern of anti-Muslim intent. (It affected only a few nations, all of which had been subject to restrictions—albeit less severe ones—in the past.) The court should have also considered Mr. Trump’s hostile statements, which post-dated as well as pre-dated his inauguration.

The court should have also considered Mr. Trump’s hostile statements, which post-dated as well as pre-dated his inauguration.

The statements are relevant because they create a strong inference that the United States would not have had this ban were it not for Mr. Trump’s hostility-based promises and his desire to be able to say he had fulfilled them. That reasoning governs in racial-discrimination cases: Even a facially race-neutral law that harms a racial minority is unconstitutional if the motivation for adopting the law was to harm that minority. The same rule should apply to claims of religious discrimination, like this one.

The majority said that this general rule of looking beyond the order’s terms, and considering the decision-maker’s statements, should be inapplicable to immigration policies. The justices disagreed over whether previous case law dictated that conclusion. But there was room in those precedents for the court to write a narrow opinion focusing on Mr. Trump’s uniquely blatant and irresponsible statements that suggested his intent as the sole decision-maker. True, such a ruling would have to have been narrow, to keep from setting a precedent for serious intrusions on executive authority in future cases.

Even a facially race-neutral law that harms a racial minority is unconstitutional if the motivation for adopting the law was to harm that minority. The same rule should apply to claims of religious discrimination.

But the risks from such an opinion would have been worth taking. The president’s statements were virtually unprecedented in modern times in explicitly labeling all members of a religion a danger to the nation. The consequences of the resulting ban are serious for those affected by it: many thousands of entirely innocent people restricted from visiting their family members, pursuing educational and other opportunities, etc.

And the consequences of the statements extend further, poisoning the culture in the country for Muslims already here. Reports of anti-Muslim vandalism and other crimes have spiked in the wake of Mr. Trump’s statements.

The consequences are also harmful for religious freedom as a general principle. Republican support of Mr. Trump’s hostility to Muslims from the beginning (one March 2016 poll showed that 71 percent of Republican voters backed a temporary “total and complete shutdown” of Muslims entering the United States) has helped accelerate the perception that religious freedom is nothing more than a tool for each side to use or discard according to what supports its preferred policy positions. Progressives are selective, too, in denigrating the religious freedom of social conservatives. To preserve religious freedom as a principle, not a tool, we must enforce it for all.

Our constitutional system has many strict rules against official actions that show blatant hostility to an ethnicity, religion or other vulnerable group. The court should have adopted a strict rule here too.

There are three sources of comfort. First, the ban had narrowed and softened in significant ways by the time of version 3.0, after lower-court decisions that struck down the two previous versions. Constitutional protections did not eliminate the harms to Muslims, but they reduced them. Second, plaintiffs whose religious practices are harmed by the ban—for example, mosques or other Muslim organizations seeking to welcome immigrants as members—may still have claims under the Religious Freedom Restoration Act, which has no exception for immigration cases.

Finally, given the court majority’s clear emphasis on the immigration context, we can have reasonable confidence that courts will still act decisively to forbid official animus against Muslims in domestic matters: hostile local resistance to mosques, officials’ attacks on copies of the Quran and so forth. The travel ban decision specifically endorses, and must not be read to undermine, that bedrock principle.

Thomas C. Berg is James L. Oberstar Professor of Law and Public Policy at the University of St. Thomas (Minnesota), where he teaches religious liberty and intellectual property, among other subjects, and directs a religious-liberty appellate clinic.