Dude left his son and wife for the ghost of Jean Grey
And then the writers tried to WHITEWASH it...real fukking gay.
The writers tried to whitewash it because they weren't the ones who made those decisions to begin with. The Madelyne Pryor breakup was all a result of editorial mandate. The top brass at Marvel saw how popular X-men was getting so they retconned Jean's death on the moon and demanded that a spinoff with the original 5 be made in order to capitalize on the mutant craze without telling the original dude who was writing the actual series. The original dude writing the books at the time (Chris Claremont) initially had him marry Madelyne in order to give the character a happy ending and permanently write him out of the series-- he was going to get married, move on, and stay that way, only occasionally coming in to help out periodically in case of emergencies.
The higher-ups made sure that Claremont didn't find out what they had done to the character for the sake of having another X-book out until it was too late for him to prevent or change anything. When Claremont found out, he was disgusted to the point of wanting to quit the series.
While better stuff eventually came out of X-factor later on when the Simonsons took over (Archangel, Apocalypse, etc.), the first several issues are generally agreed to be seriously problematic.
They destroyed the pathos of the Dark Phoenix Saga, character assassinated Scott for the sake of $$$, and their initial "Ghostbusters-like"premise (they initially posed as normal humans who hunted mutants in order to capture and study them, while secretly taking them in to train them) makes no sense when they have a veteran Avenger (Beast) and a ridiculously wealthy dude with a public identity (Angel) who could have easily used their resources and Avengers contacts to create a legitimate organization to help mutants. And at no point does anyone else in the story tell Scott to man up and call his wife. Basically everyone was hella out of character in that series for the sake of having another X-men book they could market and make bank off of.
tl;dr: Scott leaving his wife and kid was grossly out of character and basically a result of sloppy writing for the sake of the $$$ that came with having another X-book out. The original writers had nothing to do with it.