I'm surprised that this is being dropped, but the "Send to Kindle"[0] feature is still supported. I would imagine that the email servers (and whatever other behind-the-scenes cruft it requires) to relay files to individual Kindle devices is a much bigger maintenance burden and "piracy" enabler than transferring via USB.
I'm a huge user of the Send to Kindle feature via my Calibre library too, so this has me pretty bummed and pessimistic for the future. I guess if the worst comes to pass, I can just look into jailbreaking or getting any of the zillion other Android-based eReaders from AliExpress.