It's pretty obvious that Watson had already made up his mind and wrote most, if not all of his decision before even hearing arguments in this case. 
His decision was not based on the content of the order at all. He left out the fact that those 6 countries were on the list because they are either unwilling or unable to provide the necessary information needed to properly vet immigrants from their country. 
By Watson's logic, Trump can do no harm to Muslims in any way by executive order because of statements he made during the campaign that Watson believes were discriminatory.
Trump is merely trying to keep radical terrorism out of the country. They just happen to be Muslim.