If a cyst must be removed, and therefore an unintended abortion is the result, it is allowable because the intention was not to end a life but to save a life. It’s then up to the woman, her family and her doctors to decide what is the best course for her. It’s not that the zygote is not human, it’s a question of why the cyst is removed.
It’s actually a bit more complicated. See the second document from the CDF that I posted above.
Many Catholics assume that certain specific examples of double effect are actually Church doctrine, but that is generally not the case. For example, even now students at Catholic high schools often are taught that there is a moral difference in ectopic pregancies between a salpingostomy and salpingectomy. But that distinction has never been promoted by the Church iteself and has always had many critics.
Medicine has also long passed it by. If you look to the CHA or the National Catholic Bioethics Center you will see that the issue has become theologically murky indeed. Ectopic pregnancies are now detected and terminated before the mother is in any imminent danger, and modern medicine makes the likelihood of maternal death lower in general.
The problem is that for double effect to be licit, the consequences must either carry the same moral weight, or be reasonably unforeseen.
If we take the position that every zygote is a human person, not just human life, then removal for, say, the purposes of fertility, would generally not be licit. The procedure is not because the mother’s life is in danger, the procedure is because the mother desires children, but the procedure means death to the zygote, even though there is no existing mortal peril.
These sorts of cysts are often removed pre-emptively because they have a higher probability of becoming cancerous. Again, if the cyst is a human being, not simply human life, where is the moral symmetry? I’m killing you because there is an elevated chance you could put my health at risk some time in the future?
To be clear. I am in agreement with the Church’s position on the Human Embryo. That said, I would never presume to pass judgement on other Catholics who find themselves in difficult situations. My obligation is simply to try my best to love them all as I love myself.
My only point is that the Church’s position is nuanced (see the doctrinal instruction above) and that this nuance serves some important purposes. It keeps Church teaching from falling at odds with modern biology and it leaves some latitude for the individual moral conscience (a gift we each receive from God) in some of the most difficult moral and ethical situations that human beings can face.