[1]: https://news.ycombinator.com/item?id=7838663
[2]: http://imranontech.com/2008/04/01/the-origin-of-hacker/
^ That is by no means a settled debate. Even in the comments section of the link you produce as evidence ( http://imranontech.com/2008/04/01/the-origin-of-hacker/ ) there is plenty of debate on the conclusions.
You should have just ended after suggesting that hte debate is pretty much unresolvable. :-D
And just to be up front about the whole thing -- I prefer the non-malicious use of the term. Hollywood has a pernicious tendency to stereotype anything and everything, and the fact that that culture is mostly responsible for promoting the malicious use of the term means that in my book they shouldn't get to determine its meaning.
Again, unresolvable. :D
"Cracker" is a very specific term that relates to those who hack static files, by breaking encryption, etc. A cracker might discover a back-door, but if they exploit it to access a running server, that's not cracking, that's hacking.
Hacker is a general term which can apply to white-hat hackers and black-hat hackers alike. It means anyone that breaks things apart to see how they work, then puts them back together in a way that does something they weren't designed to do. That could mean getting Mario to run on a Ti-83+, or getting root on someone else's server.
Unfortunately, while we have the words cracker and phreaker for particular subsets of hacking, the subset that tends to get itself a lot of negative publicity by hacking into computers doesn't have any special name associated with it.
As a hacker (in the HN sense), I don't have a problem with this. The meaning is always pretty clear from the context. All it means is if you say "I'm a hacker" to someone, you better be prepared to explain what you mean. But if you say that, you're setting yourself up for a pretty geeky conversation anyway, which many won't appreciate.
Hackers that hack into computers aren't necessarily all black hat either. It's perhaps less common nowadays, but a lot of hackers just do it to see if they can, or to see what they can find on networks, simply out of curiosity. The latter is the defining characteristic of all hackers.