This isn't that bad. A company will never announce internally whether or not someone got fired or is just quitting (a well-run one, at least), with some exceptions (e.g. the executive level). Companies will just say something to the effect of: someone is moving on from the company. There's nothing wrong with using "graduating" in place of "moving on from the company", "leaving," "moving on to a different opportunity," etc.
I guess, though moving on sounds a bit more neutral than graduating. One sounds like 'they didn't quite fit in and hence they're parting ways' and one sounds like 'they're a bit too good for this place, so now they're off to Google/Apple/some other company with a good reputation'.
Neither is accurate. Everyone knows that saying someone is moving on does not imply "they didn't quite fit in." My point is, companies will try to be polite about announcing that people are leaving, so "graduating" is not that bad of a euphemism.
The flaw in your reasoning is assuming that companies have an obligation (or otherwise should) be completely transparent to employees (to present the complete reality). If you think they should, well, you just about disagree with 99.9% of companies ever (including successful ones).
