My own experience makes me suspect the same thing. I used to work for a company that was, at the time, trying to develop a privacy-enhancing product (ironically enough...) which did something
somewhat similar (although not on the size of this fuckup -- they'd be intercepting, but not tampering with, encrypted traffic, and storing encrypted private data).
Virtually everyone in the engineering team raised a flag when the imbec...uhm, the Product Manager came up with the idea. We pointed out that a) this burdens us with the responsibility of storing sensitive data which can, at least, have significant legal implications and that b) even if it's encrypted data, it may be a little hard to market a privacy device that works by uploading user data to our server as a first step without being transparent about the whole process. Oh, and c) that the data recovery mechanism he proposed (which involved storing the users' private keys on our servers as well, just in case they lost their precious little gimmick) was, in this case, entirely retarded.
The whole thing didn't even make it to Legal, because everyone in the decision tree just thought that since there's no plaintext data being stored, there's no potential for a lawsuit (and when we told the PM about Lavabit, he came back two hours later saying he Googled it and that we're covered since we're not an e-mail provider). The bright heads in Marketing weren't exactly sure about the whole transparency thing. They thought we should keep it simple and just tell people that their data is safely encrypted and be done with it, because end-users don't need to know about tech mumbo-jumbo like encryption keys and all that.
I don't work there anymore (thank God) and they haven't launched in the meantime, but when I left, they were basically working on implementing this clusterfuck.
I'm sorry I can't be more specific than this (for obvious reasons, I hope). The point is, however, that decisions as complex as these (there's a stack of paperwork thicker than the Osbourne-1 involved in preloading anything on a laptop) are made through an elaborate process, not made "by mistake".
Someone knew there was a problem. The problem may have ended up misunderstood or washed out along the decision chain (although I find that fairly unlikely), but someone, at some point, decided this was ok.