This kind of disturbingness is more about expectations than the actual content. If this was meant to be a dark story in the first place, i think its fine. Otherwise you risk alienating your readers.
That said, i don't think the part about the boy forgetting everything and living like normal is a good plot point. While its true victims of traumatic events like that may block the memories, those memories usually get reawakened by certain triggers. I don't think he'd be able to live alongside his step-father like nothing ever occurred, unless he made a conscious decision to ignore that ever happened out of fear or maybe because he was desperate not to lose a father figure and a good owner.
For a less "disturbing" alternative in case you need one, or at least something that might make the step-father slightly more sympathetic, you could change the trauma of being raped by him to instead having watched his entire family get killed (its still "disturbing" but we all know readers are far more ok with gore and murder than rape) which eventually led him to be captured and sold as a slave. While leading a good life with this new owner he blocks off the trauma from his mind, until at some point in it gets reawakened for some reason. He decides to investigate what happened and eventually finds out it was his father figure (through his hand or through his orders) that killed his family in the first place. Then, filled with guilt, at some point after the deed, he searches for the boy, buys him and raises as his own as a form to appease his guilt and gain some redemption. Naturally add some possible adjustments to fit your story better.