There is, in fact, evidence to show that it is discriminatory.  It's discussed in Part VII of the decision, where Trump's desire to enact a Muslim ban and numerous statements by Trump and people in his circle (e.g., Giuliani) indicating that this meant to be the ban.

Also, this wasn't a ruling on the merits, it was an attempt to remove the restraining order.  The government failed to show irreparable harm would be caused, and instead argued that the courts had no jurisdiction to review these decisions, which is plainly false.