The problem is that it was originally used to mean "someone who is really knowledgeable with a subject and hacks around" -- and then got picked up to mean "someone who breaks into computers." Only afterwards did the security community try to push "cracker" as an alternate term, and it never caught on (and I suspect never will).
I work in the computer security profession and I use the term hacker - because now that has become one of its accepted definitions. It's listed in the Old English Dictionary:
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b. A person who uses his skill with computers to try to gain unauthorized access to computer files or networks. colloq.
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