I don't think the decision is anything to do with the "Muslim Ban" element of complaints against this Executive Order. Seems to be more to do with the perceived damages caused to the States -- from loss of freedom to travel to the residents of the States, along with "employment, education, business, family relations... as well as injury to the States' operations, tax bases, and public funds."
https://www.documentcloud.org/documents/3446391-Robart-Order.html
Sure, it's a badly-targeted order (as has been pointed out more than a few times, terrorist attacks against the US have exclusively come from other countries) and can be perceived as religious discrimination, but -- for the moment at least -- this is not the problem with Trump's EO.