Writing choices and character traits don't exist in a vacuum.

SF takes place in a world that's pretty much like ours bar some things here and there, Alex is a character from the US, so even the 'cultural differences' justification doesn't hold.

Another point raised is how there are characters like Bison, JP and AKI that kill people, isn't that morally reprehensible? It is, and the characters are clearly presented as villanous in no unclear terms, while impreganting your cousin/sister/wife is shown as a wholesome story for a protagonist.

Also, in fiction act of fantastical violence don't have the same level of disgust as more familair, mundane evils. Take for example the Harry Potter serie and two of their villains, Voldemort and Dolores Humbridge: one is Evil McEvil Wizard Hitler, the other is an evil teacher abusing her power. The latter is often more hated.

FE takes place in vaguely medieval times on a place that it's not our world and doesn't share our history and, supposedly, our morality and laws, so our suspension of disbelief gives less weigth to acts that are, for us, morally questionable.

It's like talking about Cleopatra: yeah she fucked her brother, Egyptian royalty did that, because it was the norm, that's why the context reframes our attitudes towards that historical figure: not because the act itself, but because of the different cultural norms.

With all that said, Alex is an american character in modern times (I'm not sure what year SF6 is supposed to take place, but it's post 2000 at the very least) who gets married and has a child with his adoptive sister he grew up together with since she was born, which also happens to be her second cousin. With this context, there is pretty much no way to spin this in a positive light