@semck, thanks for the fine post.
I do tend to view morality - moral intuition, as you called it, as not tapping some universal morality but rather a function of what evolution has found, through trial and error, to work... and continues to fine tune. Clearly there are creatures that exist on a completely different set of moral values - the black widow or praying mantis that kills the male after sex, the shark which is not above cannibalism (indeed neither are humans, given the appropriate survival imperative), ticks that only survive as parasites, etc. And within humankind, there are strong tendencies for behavior and strategies that are common (and that I promote) - social cooperation and valuing the community, for example... but these are also anything but universal. Many religious people would say that is due to the presence of evil... I use the word "evil" as shorthand from time to time but I doubt it's existence as a separate force... I see it more as an ignorant short-sighted sociopathic approach where a more cooperative love-based approach simply works better and is more fulfilling (for most). Anyway... I do completely agree with your analysis otherwise - as far as the difficulties (and why) in talking about morality or reason with others of a radically different perspective or basis for their beliefs. In a rough (everyday functional) sense, I believe morality to be more or less universal in humans thanks to our social history/imprinting... i.e. it clearly transcends details such as religious/philosophical beliefs - and *is* as you note, on a more basic level. You would differ as to what that basic level is (see above) - but we agree there is one. (And despite my view that there is no absolute universal morality - I find the one that most people reference [being kind, etc.] to be pretty useful and emotionally rewarding... so I embrace it). I don't believe that such moral intuition extends necessarily to the level of it's wrong to abort an embryo in all situations period... and I read you as basically agreeing.
So on to heuristic arguments, since that is what we're left with. I believe, in its most bare sense, that a woman has a right to her body that is absolute... despite the fact that the fetus becomes increasingly complex over time and the transition from potential person to realized person is gradational and thus not clear like an on-off switch. Upon birth, the mother's body is no longer part of the equation - so I don't have much sympathy for infanticide (though in cases of severe deformity and disfunction concepts of euthanasia may come into play). To me, as far as rights of the mother over her body, this line - birth - is a clear one. Just to be clear, I don't support destructive elective abortion in the 3rd trimester when there is no health/safety imperative arguing for it. (i.e. when possible, deliver and try to save a viable fetus - assuming it does not put the mother at risk). The medical focus should always the health of the woman... and the fetus is secondary, though still important. Health of the mother trumps fetus. Obviously if the mother decides to risk her life in a birth attempt that is for some medical reason particularly dangerous for her, than that is her right (and could be seen as brave or foolish, depending on what kind of risk we're talking about).
Being that I find no elemental difference in value between a human life and say a dolphin's life - other than a recognized bias for my own species (born of survival instinct and not having any objective value - i.e. other species would have a similar but opposing view on their relative worth). My valuing of a human life is most intense in regards to myself and within my own family - naturally. I believe that an individual is best suited, for this reason, to judge what they should do in regards to themselves, their family, their extended family/friends, their subculture, their society... in expanding circles of less subjective importance based on less personal investment. So - decisions such as destructive abortion in cases where it is an embryo and is not viable (or as described above in cases of health threat) should be completely left to the mother and whoever she wants to consult with. I cannot think of anyone better qualified for such a decision: emotionally, practically (knowing her specific situation), and morally (since that is debatable).
If it was me in that situation... well, if it was me being consulted, my valuation would be based on: 1) health (physical, emotional, mental) of mother, and 2) health of embryo/fetus. In the event of abortion, I have no problem with an abortion in the first 2 trimesters from a standpoint of the value of the embryo. Embryos are generally pretty easy to come by, should one want one and don't have fertility problems (i.e. no threat to the survival of the family or the society or species), and at that point are less aware than a field mouse - and though I may be squeamish about killing a field mouse - I'm going to do it if there is a reason to that I find compelling. Further - from a standpoint of adoption... there is no shortage of kids needing to be adopted. So it's not like we would be filling some poor couple's need that has no other alternative. Indeed - by aborting, we are, in essence, helping increase the chance that a child currently in need of adoption will be adopted. (by us not increasing the already abundant supply). That last, in itself, is a compelling reason to *not* take a pregnancy to term with the intent of giving up for adoption.
I kind of wandered a bit - but I hope what I wrote was somewhat on target for what you were looking for.