Is agreeing with a colleague, who is believed to be an innovator (mubtadi’), on his statement, “I do not believe in ‘bid‘i’ or ‘sunni’; we are all Muslims,” out of fear of harming him—knowing that the speaker is a Sunni and proud of it—likely to lead to apostasy (kufr)?

What you experienced is not considered apostasy, especially since your heart is at peace with faith. A person suffering from intrusive thoughts (waswas) must turn away from thinking about apostasy, because words that might be interpreted as disbelief are not considered disbelief unless the speaker intends them as such. One should act in a way that keeps the Muslim within the fold of Islam.