It looks like The Verge has fixed the sentence to "The court specifically ruled on Darweesh and Alshawi’s petition; other similarly-situated people being detained and those in transit are covered by the ruling, which is only temporary."
It is true that this doesn't stay the entire executive order. It just responds to the habeas-corpus bits for those who already made it to the US (including someone who was being placed on a plane leaving the US as the order was being made, and hopefully was allowed to get back off that plane).
"WHEREFORE, IT IS HEREBY ORDERED that the respondents, their officers, agents, servants, employees, attorneys, and all members and persons acting in concert or participation with than, from the date of this Order, are
ENJOINED AND RESTRAINED from, in any manner or by any means, removing individuals with refugee applications approved by U.S. Citizenship and Immigration Services as part of the U.S. Refugee Admissions Program, holders of valid immigrant and non-immigrant visas, and other individuals from Iraq, Syria, Iran, Sudan, Libya, Somalia, and Yemen legally authorized to enter the United States."