This is a specific example of a broader question of an individual privacy, which also applies to living individuals. I think this is an area where genealogy software falls short. I would like to know if any software handles sensitive information in a more efficient manner.
On another thought, what is the source of the information of one brother fathering the other brother's children? Is it noted on the birth certificates or some other official document? As all information should be related to the source documents, maybe you could build one tree from official documents and one with the other source. The "correct" one will be the officially documented one. It would be good to keep the other one, assuming the source can be trusted, for medical reasons should any of the descendants need it.
Last thought, if this information is true, do not let it die. In my wife's family there are some family secrets that people took to their grave which has been a great detriment to the family history. We all have things that our ancestors did that we may not be proud of but at some point people are removed enough to accept their ancestors objectively.