It’s important to remember that SCOTUS  action is only a preliminary round. The Supreme Court was considering lower-court  '...rulings that had held the proposed travel ban to be such an egregious infringement on religious rights that it needed to be prevented from taking effect on an immediate, emergency basis.'

SCOTUS both agreed and disagreed with this conclusion. On one hand, Trump cannot ban from entry anyone with a “bona fide relationship” to the United States. That includes foreigners with a job, spouse, or school in America. On the other hand, citizens of certain Muslim-majority countries without such a connection now can be barred from entry, effective immediately. Many refugees may fall into this category. 

This all might be moot,  the 90 days expire the end of September; October starts a new court session.