I think the fundamental issue is this:
We have a separate category for women because without it, no women would even make the Olympic Games (with the exception of equestrian). Most of the women's world records, even doped, lie outside the top 5000 times run by men. Radcliffe's marathon WR, for instance, is beaten by between 250 and 300 men per year. Without a women's category, elite sport would be exclusively male.
That premise hopefully agreed, we then see that the presence of the Y-chromosome is THE single greatest genetic "advantage" a person can have. That doesn't mean that all men outperform all women, but it means that for elite sport discussion, that Y-chromosome, and specifically the SRY gene on it, which directs the formation of testes and the production of Testosterone, is a key criteria on which to separate people into categories.
Now, for various biological reasons, and I'll follow the post above up with another on the specific science of this issue, sometimes that testosterone doesn't quite "do its job", and that is when we find ourselves dealing with an athlete like Semenya.
She is NOT a man. And it is enormously disrespectful to call her "it", or "he". Nor should any of your wrath or frustration be directed towards her. She's running per the rules that were changed by CAS, and it is they who should shoulder the responsibility for the mess that is the women's 800m.
So going back to the premise that women's sport is the PROTECTED category, and that this protection must exist because of the insurmountable and powerful effects of testosterone, my opinion on this is that it is fair and correct to set an upper limit for that testosterone, which is what the sport had before CAS did away with it.
The advantage enjoyed by a Semenya is not the same as the one enjoyed by say, Usain Bolt, or LeBron James, or Michael Phelps, because we don't compete in categories of fast-twitch fiber, or height, or foot size (pick your over simplification for performance here). So Semenya has a genetic advantage, by virtue of A) having a Y-chromosome and testes, and B) being unable to use that T and/or one of its derivatives enough to have developed fully male.
In that regard, if you approached it from the other direction, you could, relatively accurately, say that Semenya has a disadvantage compared to other males with XY and testosterone, because unlike them she cannot fully use T (and/or a derivative - depends on the exact condition).
however, as it stands, her "advantage" is seen and responded to, rather than the "disadvantage" and she competes as a woman. It means that she identifies as a woman, is female, but my contention and the thing that sport might have to address is whether someone who identifies as one gender is necessarily able to compete as that gender.
That's where the hyperandrogenic guidelines tried to find a compromise - they set what was a very generous upper limit of 10, which is much higher than most females, but alas, CAS in their wisdom decided to do away with it.
Semenya, and a few others, are now providing how ludicrous CAS' decision was.
One final point - there is a position here, made by a good few people who I really respect, which holds that Semenya and others did not choose this, they have not cheated, and it would be inhumane/unethical and violation of human rights to force upon someone a medical intervention that is not for health reasons, and to prevent them from participating in sport if they don't.
That's an argument I don't agree with, but I can see that people may hold, and are entitled to. It's not wrong, and it is possible to have two disagreeing positions without being wrong on either. What is wrong is to compare Semenya's advantage to Bolt's, or Phelps', because their genetic "luck" doesn't put them into a different category, and also, Semenya's "advantage" is actually a "disadvantage" to competing, as I said.
Final point, Semenya will run the 400 and 800 in Rio, and she will win both. It will cause a Sh!Tstorom of note, and I'm South African, so that will be a lot of fun (said nobody ever) and arguments. So this is a long post, sorry, and the article where I interview Harper is long, but really, this is going to be a big issue, and it pays to know a little before leaping into it! Besides, I thin kit's a really interesting subject.