As Martini has pointed out, the principle of double effect often employed in Catholic moral theology can plausibly be invoked here. The argument is that, so long as the couples in question do not intend the contraceptive effect of condom use as either a means or an end, there's nothing intrinsically wrong with condom use for the sake of disease prevention. As I understand it, the Vatican's problem with condom use in such circumstances is not that it's intrinsically wrong, but that the unintended, broader effects of promoting a policy of condom use for such a purpose would outweigh its intended, good effect for individual couples. (If I'm wrong about that, somebody please correct me.)
The Vatican has a good point. Given human lust, and the heedlessness often induced by lust, a sexual practice initially adopted for good reason often spawns related practices that make the cure worse than the disease. The fact is that the more sex people think they can have without bad consequences, the more sex they are going to have with more partners, and thus the more bad consequences they are likely to cause. This is why I believe the Vatican is right to oppose throwing condoms at people in areas where AIDS is epidemic. Still, a good case can be made that it would be at best imprudent to insist that the couples in question decline the condom option as due "religious submission" to what amounts to a broad pastoral judgment. So while I unreservedly profess the teaching of the Catholic Church that direct, intended interruption of the generative process is intrinsically evil, I also believe that the issue of condom use to prevent transmission of fatal diseases should be left to the consciences of the couples themselves. And so I agree with Martini on this, at least insofar as I understand his position. In any case, the issue seems to me to be pastoral not doctrinal.
The doctrinal issue arises on the other main point Martini has made: we cannot say with certainty that that each and every human conceptus is a human person from the moment of conception. Let it be granted that every distinct, individual human being is a human person; Martini's claim is that, prior to the developmental stage when a fertilized egg would "twin" if it's going to twin, we cannot say that such a blastocyst is or contains any distinct, individual human being and thus a human person. It follows that, in our present state of scientific knowledge, we cannot say that every blastocyst is a human person. Again, I believe that is correct.
But I would also insist that nothing, as yet, logically follows about how we should behave toward the conceptus. Given that most concepti are not going to twin, most are human persons; and even if the ones that will twin are not or do not contain human persons, there are other reasons why they should not be eliminated or used merely as means to good ends, such as stem-cell research. For one thing, such acts would be contraceptive, which is intrinsically evil; for another, we don't know that such concepti aren't or don't contain human persons. If we err in such a matter, it should be on the side of caution. The Church has always taught as much; moral theologians call it "tutiorism", i.e., the principle that it's best to be on the safer (tutior) side. In this case that seems undeniable. For scientific progress may eventually yield enough knowledge to enable metaphysicians to conclude that every conceptus either is a human person or contains at least one. In the 19th century, genetics and neonatology progressed to the point where the Church became more certain than before that at least most early-stage babies in the womb are human persons. She tightened her pastoral policy about abortion accordingly.
As I understand him, Martini doesn't seem sensitive enough to such concerns. The Vatican is right to dislike that. But he has at least outlined a "progressive" position that is not heretical. For that, the Church owes him a lot.