To briefly summarize, the author uses the arguments put forward by Don Marquis regarding morality as it relates to abortion (he opposes it in most cases), and suggests that Pope Francis (being the wonderfully different and completely expected grand reformer of the Catholic Church) should rethink his position on abortion in cases of rape.
Those are arguments which make a lot of sense as applied to the State within an American legal framework. They make somewhat less sense in a Catholic moral framework.
As a disclaimer, I don't have a problem with his reasoning. In fact, I really like Marquis' arguments on abortion which are being used here. The problem is with the context in which that reasoning is applied.
The argument makes sense in the context of a legal framework in which the purpose of law is to adjudicate disputes between parties and ensure that minimum ethical obligations are met. If the author is only arguing that Pope Francis ought to reconsider legalizing abortion in cases of rape, then fair enough. He has a good argument in that context. But the author seems to be arguing within both contexts, so let's look at the other context.
The purpose of Catholic moral teaching is NOT merely some legalistic way to ensure that minimum ethical obligations are met. Catholic moral teaching calls us all above and beyond minimum ethical obligations to practice heroic virtue. As a Catholic moral teacher, Pope Francis has a responsibility to reiterate that call to heroic virtue. Within a Catholic moral framework, it would be counter to the very purpose of Catholic moral teaching to change the moral teaching on abortion (or premarital sex, which also asks us to go far above and beyond what state law would require) for the reasons given by the author.
Of course, the author seems to assume that the purpose of Catholic moral teaching is not so lofty as all that when he writes,
"It is hard to claim that a rape victim has a moral duty to bring to term a pregnancy forced on her by rape, even if we assume that there is a fully human person present from the moment of conception. We might admire someone who has the heroic generosity to do this, but talk of murder is out of place."
He specifically excludes the possibility that we have a moral obligation to heroic virtue here. That's simply not true in the context of Catholic moral teaching, particularly as it relates to sex and children. He is asking Pope Francis to accept a view of morality in open conflict with the moral message of the Gospels. Christ calls us repeatedly to what would be seen as heroically virtuous (supererogatory) behaviors and to "Love one another as I have loved you." Christ loved us with a heroic generosity far beyond any moral obligation he had to us. And since Christ points out that if we love him, we will keep his commands, I have to conclude that our love should draw us to supererogatory behaviors as well. And if we strive to emulate Christ (as Christians are called to do), that should draw us to supererogatory behaviors as well.
Because Pope Francis is obviously a man who strives to live the Gospel message, I doubt that a call for him to stop taking that message so seriously (especially as it relates to the most vulnerable) is going to be remotely persuasive. Nor should it be. Pope Francis seems to think that we need to have a healthy pastoral approach to women who are in difficult circumstances while not backing away from the gravity of killing a child in Church teaching on morality.
So should Pope Francis rethink his position on whether or not abortion should be legal in cases of rape? Maybe so, but that's a question of his political views, a question which is properly framed in a different context than in his role as Bishop of Rome.
Should Pope Francis rethink his position on whether or not abortion is moral within the Catholic moral framework? Maybe, but the argument provided by the author is thoroughly incoherent with Catholic moral teaching from the start, so it would need to be a rethinking based on something else entirely, because the objection in this context is essentially that, "I disagree with the purpose of your moral framework and think it should be the same purpose as in a legal framework." That's just a statement of fact rather than an effective argument.
Related: How should we treat women who procure abortions in rape cases?
Since the overwhelming majority of women are getting abortions not because they really want to but because they feel forced into it (the fathers pressure them and/or withdraw support for them and/or family members refuse to assist), it's hard to say that the rape was the only factor in the decision to get an abortion in many cases.
It's often the case that circumstances were very difficult for the women who procure abortions in several ways. Poverty and a lack of support from the fathers are huge factors. I tend to think that women in these circumstances need Pope Francis' "field hospital" Church more so than the latae sententiae excommunication prescribed by Canon Law as a penalty. They need our love more so than our concerns about whether or not being raped justifies them in the eyes of the moral law.
On a personal level, I would much prefer to see a greater recognition of the role of men's failures to support the women with whom they are having sex and prescribe and publicize a latae sententiae excommunication for encouraging or coercing a woman into having an abortion. The pastoral approach of the Church on these matters can make it appear that it is guided by sexism, and while I doubt that many of the bishops are actively engaged in some sort of malicious behavior toward women, I suspect that many of them are too distant from the situations of the most vulnerable women to have a proper appreciation for how much men play a role in their decisions to procure abortions.