Most of a woman’s fertilized eggs do not implant. Why is the morning after pill wrong, then, when it simply seems to heighten a natural process of the woman’s body?
If life begins at conception, why would God make a woman’s body in such a way that most human lives (fertilized eggs) are so promptly lost? Is heaven mostly populated by those who were never born?
I will try to answer from basics upwards, so forgive me if this is a little patronising:
The morning after pill is abortifacient - it risks the destruction of human embryos
in utero. We assume that an embryo has the same moral status as any other human being, so it would be wrong for it to be killed (hence similar proscriptions against abortion and “the pill”).
The difference, however, is this.
The natural loss of embryos through failure of the reproductive process is largely inevitable and generally unintended. There is no moral obligation to prolong all lives all the time. It is unfortunate, but an accident none the less.
Interventions (such as the morning after pill) which deliberately exterminate an embryo are sinful not because of the death itself but because of the intention. The intention of taking an abortifacient treatment is to actively and purposefully kill the embryo. This is wrong. “Thou shalt not kill” &c.
Your point about the inefficiency of the human reproduction system is valid. The death rate from natural embryo death is very high indeed. (See a similar question I worried about here:
forums.catholic-questions.org/showthread.php?t=650196).
I am unsure as to why God made humans this way. I am sure that this is some hidden wisdom in the design. Certainly this is not the only inefficiency in the human body.
It is not necessarily the case that the afterlife is full of deceased embryos, as we do not know the exact point at which ensoulment occurs. That doesn’t mean it is acceptable to kill embryos (the “soul” is greater than and distinct from “life”).