Yes, but you are forgetting that relativism and frame of reference are the only way we can understand the world. You are looking from your point of view, down the sight of your sniper-rifle of righteousness, not unlike the ranting religious fanatics that tell me I'm going to Hell every, single, god, damned, freaking, day when I pass by Turlington or Library West.
Did I say that cannibalism was acceptable? No.
Did I say that human sacrifice was okay? No.
Did I say that wife burning was accepable? No.
Did I say that stoning rape victims was okay? No.
Did I say that slavery was acceptable? No
Did I say that incest was acceptable? No, in fact, I said it was wrong.
Now, do you even realize that the whole genetic thing is really only a series of reinforcing bad traits and reinforcing good traits further than they already were? It isn't that single instance inbreeding (as opposed to merely incest) is more likely to cause defects, it is going to reinforce the family's traits, good, bad, neutral. Sure there is an increased possibility to have certain genetic problems, but it isn't assured. I'm still not condoing incest, but it seems you are misinformed or wildly fanatical.
As to something being fundamentally exploitative, that is debateable, as one would need to know the circumstances before making a judgement on, oh... say... ANYTHING AND EVERYTHING.
And considering the open-ended nature of the story, it could be anything from totally filial love to mildly romantic to sexual to even more extreme (obviously) exploitative relations.
"The story is fantastic, except for the incest, but that's a pretty minor part of the story." That sounds pretty inaccurate to me, it sounds more like you or whoever posted that are missing the point that the game revolves around the level of love between the brother and sister (as I listed off before). And personally I believe that pedophilia (especially to the degree of Lolita) is worse than incest, for various reasons that I won't extrapolate on because you would harp about those too.
And, no, it isn't a perfectly relevant point, because you are mixing up the concept here. The idea is that beating up old people or having sex with kittnes for shits and giggles is wrong on all levels, whereas there is limited (NOTE I SAID LIMITED) possible (NOTE I SAID POSSIBLE) to concieve merit in the idea of a sibling love that may or may not be at "appropriate" levels. But that brings us back to the cultural frame of refence point, now doesn't it?