This must be a bug that should be corrected (I hope) in the first patch.
The expanded manual suggests that the deletion of career stats should occur if you de-select an option in the import dialog (sorry, at work, don't have it in front of me). I discovered yesterday while trying to set up a historical league that this function wasn't working, which was a bit frustrating. After exploring the interface for what seemed like hours, I could find nothing like the simple "press the button and career stats are gone" feature in OOTP 6.5.
Until this feature is implemented, I won't be doing any historical leagues, because I'm a neurotic perfectionist...