" It has explicit exceptions for "religious minorities"."
That doesn't make his EO illegal, and doesn't contradict the commenters statement.
The exception for religious minorities is clear: they are targeted in genocidal acts.
Christians, Yazidis and others face acutely disproportionate and targeted violence because of their religion - so in this case, it's warranted.
The Yazidis in particular, faced outright genocide - ISIS came for them, killed the men, took the women and children into slavery, those that could flee, fled.
The are a persecuted minority group, and I don't think anyone would question the need there.
Governments around the world including the US make special arrangements for persecuted minority groups - I don't think anyone has a problem with this.