Não, Carl não foi estuprado. Não no programa ou na história em quadrinhos.
De Zap 2 It artigo sobre o episódio de TV:
"That scene has always been a really difficult one," Kirkman tells TVLine. "When I was writing the original comics, in the panel description for artist Charlie Adlard I [wrote], 'Carl is on his back, and the guy is pulling his paints off -- but don't worry Charlie, he's not going to get raped!' I actually included that in the panel description because it is such a heavy and dark scene, and I didn't want Charlie to be freaking out while he was trying to draw that.
Do número 58 de The Walking Dead, na caixa anteriormente (a tentativa de estupro foi o número 57)
After a man tried to rape Carl, Rick brutally murdered him in front of Carl's eyes.
(itálico meu para ênfase.)
O site ComicBook.com tem uma comparação entre os quadrinhos e o show da cena aqui .