Yes, I agree about what the Order says, but we also have to be clear of where the concern comes from.  

Trump campaigned with a proposal to actually impose a Muslim ban, and there is no evidence that there is any source of "terror" from these countries that cannot be prevented from the normal vetting processes.  Considering all the facts, this Order seems like nothing but a masked attempt to ban Muslims.  The likely knew that they could never succeed with a full ban, so they cooked up this alternative.