Actually, you’re the one who’s mistaken — history does support the benign view. As you note, the term hacker dates back even to the Tech Model Railroad Club. The term was generalized to include all sorts of neat but benign tomfoolery (http://en.wikipedia.org/wiki/MIT_hack) including white hat phone phreaking. At MIT, there’s definitely always been a sense that hacking has a code of ethics and that people who do bad things under the guise of hacking aren’t hacking at all.
The Tech’s 1963 reference to malicious phreakers as hackers is the same as modern day references to crackers as hackers: a mistake.