Well AFAIK Bohr was considered one of the greatest physicists of his time and a lot of students would be vying to be able to do their PHD with him. So not only did Jaynes not care about his status but he also thought with his own brain and came to the conclusion that Bohr had a flawed POV.

I read that to mean that the respect was for Jaynes' integrity, and not for his specific point of view.