If Amazon acquisition of Zappos shoes is an indicator, Jeff Bezos let Tony Hsieh (CEO) continue to keep the culture. Hsieh said in past interviews that Bezos if fairly hands off. There was still some business "synergy" in the acquisition because Zappos logistics got integrated into the Amazon warehouse in Kentucky.
Whether Bezos treats Whole Foods the same probably depends on whether he has confidence in existing management. It's also possible he has ambitions to totally remake WF into something else. In that case, it doesn't matter what managers are there because Bezos wanted the Whole Foods market presence and not the management team.