The guy writes: "I was an independent contractor. No employer-employee relationship existed. Federal labor laws afforded me the right to choose when to work, where to work, how to work and what work I was to produce. There were no other work-for-hire contracts or specific performance contracts signed and I did not sign any NDA."
To carry forward with your "safe" analogy: Suppose a plumber came to your house. When he leaves, you demand to search the toolbox he brought to your house. Who's in the right here?
Of course, a private accusation of theft is not an official charge of theft, or a prosecution, or a conviction for it. If a private individual comes to you and accuses you of taking something that belongs to them, and you return it, that ought to be the end of it, unless the victim is really honked off and insists on involving the police. Once the Boys in Blue are involved, it becomes much more difficult to resolve the situation extra-judicially.
What we know is, that the owner claims there was a theft and the (lets call him) contractor offered to reimburse the owner. This does not mean that there was a theft. If I should speculate, it is rather likely that the contractor did loose a laptop, and at this point the relationship was already poisonous enough that the owner either assumes that there was a theft or tries to exploit the missing laptop.
> For the rest of it, the author doesn't have a leg to stand on. [...]
I think this strongly depends (IANAL) and the contractor should get the benefit of doubt. So for example if his .ssh/ directory is on that partition, then he may or may not have ample reason to keep the contents ( e.g. a private key for one of his servers) secret.
http://s3.amazonaws.com/InnocentBeyondAReasonableDoubt/PDF/C...
With regards to the allegations of theft, I'm not sure what the author's point is. He repeatedly says he offered to pay the owner back for the missing items. Should that mean that he can't be charged with theft? If I steal something and get caught, should I just be able to offer to pay and avoid prosecution? He repeatedly says that the missing items amount to at most a civil matter, but stealing stuff from work is not a civil matter.
For the rest of it, the author doesn't have a leg to stand on. Say instead of an encrypted partition we were talking about a safe. I kept a safe in my office, and one day I was summarily fired and escorted out of the building. I promised that there was no business information or property of my employer in that safe, then refused to hand over the combination. Should the employer leave it at that, saying "gee, if he says he didn't put any business property in the safe, I guess I just have to believe him!"
I can understand where the author is coming from (though his writing makes that difficult). The owner is clearly being a huge asshole. But the author is being naive to think that there must be something "fishy" going on. Unfortunately for him, he's on the wrong end of this story. It's so common for disgruntled employees to steal company property or damage company property that nobody is going to give him the benefit of the doubt except the jury, who is legally required to. The author repeatedly mentions the standard for conviction (beyond a reasonable doubt). However, that's not the standard for prosecution, which is closer to "more likely than not."