I heard what he said, and in giving him the benefit of the doubt, I think he was referring to how some women will experience muscle constriction to the point where insertion becomes extremely difficult. However, even if that was his intent, this thing is so blown out of proportion, there is no way he could ever explain or apologize enough. And, of course, his original point "prosecute the rapist, don't take it out on the baby" was completely lost. He was a guy who was stridently anti-abortion and I think a lot of people are going to take exception to anything he says.
In response to this news story, many anti-abortion organizations have re-released articles on studies that show that pregnancies resulting from traumatic rape are very rare. The theory is that the trauma of rape can cause hormone fluctuations that make implantation and maintenance of a pregnancy difficult. The response to this is that these studies are very well documented.
In terms of "legitimate rape", Akins was trying to differentiate between traumatic rape by a stranger versus acquaintance rape (date rape) or statutory rape (which is illegal but might be between consensual partners). A lot of people jumped to the conclusion that he thought that there were a lot of false accusations of rape.
But all this is a paper tiger. Is abortion after a rape any more justified that any other abortion? (Which is Akin's stance.) Is a woman any less in control of her reproduction decisions just because she was raped or not raped? The whole "except in cases of rape" clause is an imperfect compromise. I think it just leads more woman seeking an abortion to claim they have been raped which helps no one. Should a woman ever have to justify to a third party why she made such a difficult decision?