Well obviously. That was the whole crux of the 9th circuit ruling- that lawful permanent residents have broader due process rights, and the executive order was too broad since it didn't distinguish between permanent residents and other visa holders (or those that have no visa and are applying for one). The White House Counsel issued out guidance that the order was not to apply to permanent residents, but the 9th circuit said that guidance was not necessarily binding on any agency and so it could just circumvented, which is a fair point. The order originally should have been clear about an exception for them, as I pointed out earlier.. I knew this was going to be the legal issue:
The sections that ban entry probably should've included a caveat for people that have already been admitted (current visa holders etc), and grandfathered them in. I would expect that maybe we'll get clarification on that from the White House Counsel or maybe Trump himself. Without the clarification, there is a potential issue- I haven't researched it thoroughly yet, but the legality of restricting people who are already green card holders is questionable. There is a section in the order that allows Homeland Security to admit people on a case-by-case basis, so that section could be used as a loophole to admit the current green card holders.
People that haven't been granted entry yet, though (i.e. new immigrants), the order can restrict legally.
If I were Trump, I would just re-issue the order but with an exception for the green card holders. Of course, there's another side to this- the US District Court (in MA), ruled in the opposite direction, and declined to extend the restraining order since the executive order can arguably be read to exclude permanent residents as originally written (as the text implies that it only bars initial 'entry,' and not re-entry), and the permanent residents who had been detained were all released, so their claims are moot.
So there'll be a circuit split- whether the Supreme Court goes with MA or the 9th circuit is anyone's guess. Maybe a 4-4 if Gorsuch can't get confirmed in time. I think the safer play for Trump is just re-issue the order to specifically exclude the green card holders, and then it's on pretty solid ground. Liberal groups will re-sue anyway, but they'll probably lose that one. In its current form though... I have no idea... a 4-4 tie in the Supreme Court is not all that unlikely.