It’s not entirely illogical. Saying that an embryo is an innocent human being doesn’t necessarily decide the matter, since there are cases where it is permissible to kill an innocent human being, at least according to the Church – in cases of ectopic pregnancy, for example. (Here “kill” simply means “cause the death of”, not “murder”.)
That’s a good point, but in the case of an ectopic pregnancy, our priority is still protecting the life of the mother, knowing that we can’t save the child. And even then, we’re not allowed to kill the fetus before removing it. I don’t think we’re allowed to end a life unless it’s necessary to preserve more lives.
The fact is that if we say that women should be legally allowed to abort fetuses conceived by rape or incest, we are saying that people should have the right to kill people who depend on them, if it isn’t their fault that the dependent exists or is dependent on them. It’s not about whose fault it is. It is never, never, never about the fault of the mother or the father or anyone else. The reason we don’t abort children is that we must act to preserve people’s lives, regardless of how they came into existence.
However, you are correct that “except in cases of rape or incest” is way better than letting the other 98% of abortions go unchallenged, and we should act to end as many deaths as possible by pointing out that rape and incest only make up around 1% of abortions. Probably. Rape is under-reported, sadly, so we can’t be sure.

It’s probably a small percentage compared to the rest.
The author could be thinking that there is a moral obligation to not abort children of rape, but perhaps that there shouldn’t be a *legal *obligation. There are certain things that the law allows that are clearly and unambiguously wrong: e.g., manipulating people, lying for selfish reasons, having casual sex. I presume that there are various rationales for these omissions, many of which are sensible enough. My own opinion is that the pro-life movement should leave room for some nuance here, so long as we expose this nonsense that the pro-choice movement is mostly out to protect women whose pregnancies are killing them.
Yes, normally I do think there should be some space between our moral and legal obligations, since we can’t expect others to follow our religious beliefs. Hormonal birth control is a good example- we know it’s wrong to use it as contraception, but I don’t know of anyone who wants to outlaw it. But when it comes to killing people, it’s not really the same thing. The state must protect the people who live within its borders, and protecting their lives is the most basic level of that.
Why do some people think that that obligation changes in the case of a child conceived in rape? We’re not acting to preserve life anymore, as we were with the ectopic pregnancy. It seems like they’re saying that since a person didn’t freely choose an action, they don’t deserve the punishment, when a pregnancy isn’t simply a punishment for promiscuity. One person should never be regarded as a punishment for another. What matters isn’t that people get what they deserve, but that people- both mother and child- are protected as much as possible.
And yes, even though that’s my position, I do think we need to support people and politicians who support ending abortion except in the case of rape or incest. We shouldn’t let ourselves be divided, since again, the priority is protecting people. For that reason, my political positions are somewhat different than my personal beliefs.