I'm more upset about the fact that Mark and Eve not only split up but the fact that she told him that she never wants to see him again and that she doesn't think it would be a good idea for him to have any contact with his child. Not really fond of the idea that an ex-superhero who fell in love with the Earth's primary superhero while they were both teen superheroes, is suddenly holding it against said primary superhero because he has to respond to some dangerous shit and I'm saying that as a huge fan of the character of Atom Eve. Something else has to be going on here.
As far as the rape issue is concerned, it's certainly not my first idea of a place to go in the middle of a story-arc but the fact that Kirkman flipped the gender dynamic can lead to some interesting places in the future. For one thing, in the 6-months that Mark has been missing, is his father still the ruler of Viltrumite Empire? How will Nolan and the rest of the Viltrumites respond to their prince(?) being assaulted by another member of their race? Will it even be an issue? Robert Kirkman is an infinitely better writer than Devin Grayson, so I can wait out a few more issues to see where he intends to go with this.
Oh and let's not forget about the fact that Robot has had a 6-month head start on Mark. Where is he and what is he up too?