I don't think that some bastard turning protags mom/sister into slut is NTR, unless MC has some sexual attachment to them (i.e. incest), hence why I didn't understand the arc with the sister in this game. I could barely care. How to make it better? Well, if you don't want to see incest (or step-fantasy) you can make sister a more interesting and significant character (by appearing in FOG, giving advices and helping MC, having more interactions outside of her corruption arc, etc).
And yes, I have never watched SAO so I am completely out of context here.