There actually were two rape scenes in that series: One when Miracleman's creator, Dr. Emil Garganza, raped a Mexican gang leader's wife in front of the leader, before killing him.
Later, Johnny Bates was about to be buggered by schoolmates until he said the magic word to turn into Kid Miracleman, in the process of blowing off his assailant's genitalia.
Both of these scenes were scripted by a Mr. Alan Moore of Northhampton, England, who quite coincidentally also penned the aforementioned rape in "Watchmen" as well as alluding to sexual assaults in other series, such as "The League of Extraordinary Gentlemen."
Hmmm. Sounds like a research paper: "The Significance of Rape in the Post-Modern Comics of Alan Moore."