The decision to include green card holders seems to have been made by Steve Bannon:
https://www.vox.com/2017/1/29/14429984/trump-immigration-order-steve-bannon
"As agencies confirmed Saturday, the ban on entry into the US also applied to existing US lawful permanent residents from those seven countries — Iran, Iraq, Syria, Libya, Somalia, Sudan, and Yemen. So as many as 500,000 green card holders, many of whom have lived and worked in the US for years, suddenly learned that if they travel outside the country they may not be allowed back in (the White House says they’ll be considered only on a case-by-case basis). Some were in transit when the order was issued and detained at airports across the country upon arrival.
According to CNN’s Evan Perez and Pamela Brown, this shockingly broad move was the brainchild of White House chief strategist Steve Bannon. Remarkably, they report that when the order was released Friday, the Department of Homeland Security concluded that it wouldn’t affect green card holders. But “overnight,” this decision was overruled by the White House, with Bannon’s personal involvement. (White House chief of staff Reince Priebus may have walked this back somewhat during a television appearance Sunday, but it’s not entirely clear."
And now Bannon is on the National Security Council, with no foreign policy experience. The Chairman of the Joint Chiefs is off the Council, as is the Director of National Intelligence.
https://www.cnn.com/2017/01/29/politics/susan-rice-steve-bannon/
Well, the Director and Chairman will be invited to sit now and then.
Only a little over a week, and it seems like sheer lunacy every day....