There need be nothing inconsistent about this position. The first view, that abortion is morally impermissible, is a moral or ethical view. The second view, that each woman should be permitted to choose for herself whether to have an abortion, is a political view, one about what laws a state ought to have. The combination is therefore consistent so long as one denies that, if it is morally impermissible to do A, then it ought to be illegal to do A.

Why might one deny that claim? One might well ask why one should endorse it, but there is a better answer. Suppose one believed the following:

1. A law must be justifiable on the basis of principles that cannot reasonably be rejected by any citizen, where a rejection is "unreasonable" if it is flatly irrational or, more interestingly, based upon too many particulars of one's actual situation.
2. In particular, religious doctrine cannot figure in the justification of any law, since one's finding the appeal to any religious doctrine convincing depends too strongly upon one's actual situation, namely, one's particular religious affiliation.
3. In short: The brute fact of religious pluralism invalidates appeals to religion in the "sphere of public reason".
   

That's roughly the sort of view that is defended in John Rawls's A Theory of Justice, though I've adopted some terminology from Tim Scanlon in formulating the view (and so brought it closer, probably, to Rawls's later view, in Political Liberalism). The underlying idea, as applied to religion, is traceable to John Locke's Letter Concerning Toleration and Two Treatises on Civil Government. The latter is essentially the basis for the United States Constitution. (Indeed, large parts of the Declaration of Independence are based, fairly directly, upon the Second Treatise.) Indeed, one might regard (3) as a way of understanding both the basis and the content of the Establishment Clause.

If one held this sort of political view and also based one's moral objection to abortion on some religious ground—say, one's argument depends essentially upon the claim that life begins at conception, and one takes the ground for this claim to be "revealed truth"—then the combination of views mentioned is not only consistent but required.