I don't know what exactly Baha'u'llah's position was on nonbelievers, but I do know that Baha'is themselves completely reject the idea that someone's soul is "in danger" if he is a non believer.
Now, keeping this in mind, when Abdul Baha and Shoghi Effendi come along with the idea that "Covenant Breakers" are these zombie-like creatures who are dangerous and infected with a spiritual disease that eats away their soul, this sounds very bad. Between atheism and covenant-breaking, covenant-breaking seems much, much worse. Even if a person is fully certain there will be no consequences one way or the other, there is still the issue of what his parents and family will think: If he becomes atheist his parents will still love him, whereas if he becomes a covenant Breaker it is very possible that his parents will disown him.
This creates a culture where extreme pressure is put on people who dislike things about the Baha'i leadership to grow distant and apathetic towards the Baha'i Faith, rather than take action to challenge the leadership.