No, "hacker" really does mean "hacker"

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The earliest known use of "computer hacker" described a criminal act:

Many telephone services have been curtailed because of so-called hackers, according to Prof. Carlton Tucker, administrator of the Institute phone system. … The hackers have accomplished such things as tying up all the tie-lines between Harvard and MIT, or making long-distance calls by charging them to a local radar installation. One method involved connecting the PDP-1 computer to the phone system to search the lines until a dial tone, indicating an outside line, was found. … Because of the “hacking,” the majority of the MIT phones are “trapped.”
-- 1963-11-20 The Tech, (MIT student newspaper)

This isn't new information (other references from 2008 here and here), but I thought I'd point it out again since people continue to claim that "hacker doesn't mean criminal -- use cracker instead". There is no justification for that claim. Yes, "computer hacker" has always had the non-pejorative meaning "enthusiastic nerd", but it's also always been used to connote something nefarious; it's never been true that the prejorative sense is "wrong".

Although, the first use of the word doesn't matter too much. What matters is what people mean to say when they use the word, and how people interpret the word when they hear it. If people think "criminal" when they hear the word "hacker", then that's what it "means", no matter what the original definition says, no matter what dictionaries say, no matter what ESR says. Since the popular usage indeed implies somewhat criminal behavior, then that's what the word "hacker" means, and there's nothing you can do about it.

The thing is, "hacker" will always carry a negative connotation, in exactly the same way that "banker" or "CEO" has a negative connotation in many people's minds. Those who wield power are distrusted. An even better example is the word "witch", which will always carry a negative connotation despite the J.K. Rowlings attempt to rehabilitate the word. Those who wield "magic" will always be viewed with suspicion, hackers wield magic, hence "hacker" will always carry this special connotation.