First, a reminder of my own position. I am reasonably comfortable with abortion throughout most of the term of prengancy. I am less comfortable with late-term pregnancy, and I find partial-birth abortion despicable (and feel that it should probably be illegal but not the equivalent of murder). I have some sympathy for Steven Pinker's position that early infantacide is not much different than late-term abortion; intrinsically I think that's true, but the rapidly expanded options for third-party care for an infant changes the balances of concerns enough that infants deserve legal protection; it's not that birthing adds a sudden boost in personhood for them so much as the counterbalances (independence of the mother, body choices, etc) disappear. More deeply, while I consider humanness to begin at conception, personhood does not, and I believe that personhood is the basis on which we should base legal protections. Personhood develops slowly, starting at some threshold of brain development and only reaching remarkable, species-specific levels sometime in the first year or two after birth. There are points in development where a human is not more morally significant than any other animal, and at point we don't owe them different moral duties, any more than we would owe a (truly) brain-dead human.
Mourdock is working from a different framework; in contrast to me (also in contrast to Christian theologans, who have argued for years about the process of "ensoulment", which has some structural similarities to my notion of personhood), he seems to be (corrections welcome on this) operating from the perspective that what's important for judgement of acts is that something is a living member of our species. From such a perspective, all living humans are to be given full moral rights, and are protected from killing with similar vigour as adults are. The first reason that abortion might be permitted, from that perspective, fits the logic; if the life of the mother is in danger, either necessity or self-defense explain the permissibility of abortion. The second exemption, that of "in cases of rape", never had a strong moral argument; the unwanted pregnancy from insufficiently effective prophylactics in consensual sex doesn't have any morally significant difference from the unwanted pregnancy from a rape (even if the "sin" of consensual sex-for-pleasure is considered, it never entangles with the question of whether the issue is morally significant).
As for the exact nature of his quote, it's not significant and easily understood; the "it's god's will" is, I think, not a statement that the christian deity desires rape so much as that when life is created, it is a gift from that god, and that gift happens even in situations when the surrounding situation is unfortunate. It's a complicated position that unfortunately my fellow liberals/atheists are skewering without really understanding (always tempting, because we actively oppose both the cultural and legal interpretations that flow from the position).
I don't think we should be more bothered by Mourdock's position than we should by general anti-abortion advocate positions. It's the same problem; if you (like me) are best classified as pro-abortion (whether you follow my reasoning or some other reasoning), he's still part of the crowd of people who are aiming to shift policy in ways we find undesirable. He is being more consistent, but that consistency doesn't give him extra cred any more than we should be impressed by the consistency of other philosophies based on foreign values; so long as we are ourselves reasonably consistent (and I believe I am), we can be comfortable.