I don't speak with any particular authority on this matter, but it seems to me that a halfway house is the best approach. Do by all means change the name going forward, but leave the old repository up and available; essentially, fork the package.
No doubt the company will wish to expunge any evidence of its old name from the historical record, but that's just tough. Code was released with the company's name in, and the company chose to put it there. It happened, so it's part of the historical record; the company's desire for a quick-change act doesn't invalidate history. Perhaps the company will learn a thing or to from this about using java package names as a sub rosa form of advertising.
If you try to remove the packages under their old name from wherever it is they are currently distributed, and assuming they were distributed under a free licence, someone else in the user community may well put them back, and they'd be well entitled to do so. Such a bad faith act also makes it more likely, to my mind, that the community will continue development under the old naming scheme, instead of adopting the name change going forward.
