I read that one, and I was still [Grumble] [Grumble] at Superman for running off without telling Lois, his "you were boarding a plane" seemed very weak...
Mr. Beeto, in my opinion, explains things with a more reasonable and realistic set of reasons as to why CK/SM run off. Clark is too wimpy to say goodbye to Lois as Clark. Then when he's Superman, Lois has taken an airplane to get on a story, and if he wants to say goodbye to her as Superman, he would have to pull her off an airplane in front of everyone.
In S-II, Lex Luthor used Lois as bait to get Superman in target range of Zod et al. This makes it obvious to Superman that the villains see that Lois is someone they can use as a hostage or blackmail, to get to him.
A major plot point in "Family Reunion" is that Superman doesn't want Lois publicly associated with him anymore. In fact, Superman goes so far as to say that he won't speak with Lois anymore and requests that the Daily Planet set up a revolving pool of reporters to deal with him. (Of course, this is after Lois knows that CK=SM, so she understands Clark's reasoning here.)
So... Clark is going off on a five-year mission to Krypton. If he, as Superman, pulls Lois out of a plane just to say goodbye, then everyone will know she's special to him. And he won't be there to protect her - after all, he's off in space, headed toward the remnants of Krypton.
