It does raise an interesting question to those who are more libertarian minded. Normally Libertarians oppose Executive orders as an unconstitutional power grab, but are EO's OK if they come from a libertarian perspective? Like if President Ron Paul EO'd the federal reserve out of existence, would that be considered "bad" from a libertarian viewpoint?
When it comes to things that are just a matter of bureaucratic policy (like this EO related to Defense Department policy) I see no problem with the President altering policy. Actual legislation passed by Congress is a different matter.
A hypothetical President Paul wouldn't have authority to abolish the Fed via EO since it was created under the Federal Reserve Act, and he would obviously be called out and stopped (either by lawsuit or assassination) if he tried. If he somehow managed to pull it off, I wouldn't really mind since I don't think the Federal Reserve Act itself is Constitutional to begin with.