Maybe my perspective is warped, but I feel like the original meaning of "hacker" is gaining popularity lately. "Hackathons" have made their way into the media thanks to Facebook and Zuckerberg. And of course PG's writing and "Hacker News" are somewhat well known in the tech and startup circles.
Still it's far from the mainstream meaning. In some ways it's cool that it's not, it's almost like a secret handshake. If you know what I mean when I say "hacker" I have a little extra bit of respect for you.
Although I agree that "hacker" has a new meaning (and has for a long time), much like how the LGBT community adopts otherwise derogatory terms, I don't think we should stop using "hacker" because of outside influences; the actual meaning implied (coder or script kiddie) is often obvious thanks to the context it gets used in (CNN using "hacker" in a news title is different to when Joel Spolsky uses it, for example).
Thaumaturgy is the capability of a saint
or magician to work miracles. A practitioner
of thaumaturgy is a thaumaturge or miracle worker.
I like the spirit, but it doesn't quite have the cachet of 'hacker.'It's not specific to the coding field.
To me, a "hacker" is someone who is involved in finding ways to get systems to perform in a manner outside the intention of its design. E.g., hotrodders could be considered car hackers.