I think Damian was also testing his theory that Jon's powers manifest when he gets emotional. So he was trying to push his buttons. The continued attitude really wasn't justified though, especially the idea that Jon is dangerous because he's an alien.
Batman stepping in and handling Damian definitely helped to calm Superman down. I can understand not wanting to spend a lot of page space on it. I just found the sudden change of pace a little jarring. Superman and Batman talking about fatherhood actually felt pretty natural. Superman's initial reaction and his later conversation all seemed perfectly natural to me. The transition was pretty quick, which threw me off a little.