The EFF insinuates, without saying outright (since they must know it is false), that this is a law enforcement policy like the Computer Fraud and Abuse Act. A law enforcement policy is one where, if you're sitting at your desk, and the government thinks you've hacked into someone's computer, the government throws you in jail.
This executive order has nothing to do with domestic law enforcement, like Aaron Swartz or Kevin Mitnick or Dread Pirate Roberts or whatever. It is a foreign policy decision. The US maintains a public list, called the SDN list, of foreign entities that American citizens and companies aren't allowed to do business with. These are normally agents of governments the US doesn't like, eg. Iran and North Korea. This order adds hacking to the list of reasons why the President can put an entity on the SDN list. If, say, a Chinese defense contractor started hacking into American computers, the President can now prohibit American businesses from trading with them.
Under this order, the only way you can go to jail (that you couldn't go to jail for before) is if a) the President suspects some foreign person or company (say, a Chinese defense contractor) of hacking; b) the President decides to put that company on the SDN list; c) you know that company is now on the SDN list; and d) you buy things from, sell things to, or otherwise do commercial business with that company.
I think it's a bad idea for the executive to have the power to add people to the SDN list without judicial oversight. But they already had that power; this isn't really anything new. Claiming it is just confuses everybody.