This judge made a decision which supported the Establishment Clause as traditionally followed and Trump clearly demonstrated his intent to violate it by his policy of discrimination against Muslims. Doesn't matter who is injured or where they reside, the action itself is not Constitutional.
There is nothing in the EO about religion at all. Going by this logic means you can't apply any kind of restrictions to immigration or travel from any countries because if they happen to be majority <insert group here> you'd have discrimination of that group. That's obvious BS. There's no way you can logically claim this is discrimination against a group when there is no reference to that group in the EO and the EO doesn't apply to just that group, it applies equally to all groups.