Mr. Trump issued a new and narrower travel ban, affecting six countries, on March 6, trying to satisfy the courts by removing some of the most contentious elements of the original version.

But in a pointed decision that repeatedly invoked Mr. Trump’s public comments, the judge, Derrick K. Watson of Federal District Court in Honolulu, wrote that a “reasonable, objective observer” would view even the new order as “issued with a purpose to disfavor a particular religion, in spite of its stated, religiously neutral purpose.”