That statistic (which, btw, your linked article about Oscar Pistorius seems to have no direct relevance to) cuts both ways. I.e., if transgender people are such a very small percentage of the population, then they’re not really causing any “serious questions” whatsoever for anybody in the vast, vast majority of athletic competitions.
Transgender is a normal though very rare human condition, and it doesn’t make sense to treat transgender athletes as though they’re somehow “cheating” their way into the “wrong” competition category. Would we eliminate cisgender people from competition if they had some kind of hormonal advantage? For instance, if an older female athlete happened to have very late onset menopause and thus avoided the decline in muscle strength that usually follows it, would we bar her from competing in the same master’s category as her postmenopausal age-mates? Or would we just treat it as part of the normal variability in human genetics and physical characteristics?
IMO, if somebody officially and habitually identifies as a person of a particular gender, they’re entitled to compete in sporting events for that gender. If a very occasional transwoman athlete outperforms her competition specifically because of physical advantages due to her genetics, that’s just part of the happenstance of sport.
If top-quality transwomen athletes somehow become so numerous that they’re significantly shutting out ciswomen athletes from sports victories, then it will be feasible and justifiable to create a separate competition category for them, and the problem will solve itself. But I seriously doubt that’s ever going to happen, due to the very low incidence of transgender in the population. And unless and until it does, the natural place for transwomen to compete is in the same category as other women.
Just as heterosexual men need to learn to deal with the fact that a woman they’re attracted to might possibly turn out to have (or to have formerly had) a penis, ciswomen athletes need to learn to deal with the fact that a woman they’re competing against might possibly turn out to have unusually high muscle mass or aerobic capacity or whatever, due to having been born with a penis.
If you personally don’t want to date, or compete against, a transwoman, you’re free to withdraw from that situation. But you don’t get to tell her that she can’t or shouldn’t do the same things that other women are allowed to do, just because you personally would rather encounter only ciswomen in your pool of potential dates or competitors.