First off, I'm a guy, so I wouldn't need to use this myself, obviously. However, I have two young daughters to fend for and protect. So, this is definitely on my radar. My two girls will absolutely learn to protect themselves. And I absolutely plan to be there to protect them. But---you never know what circumstances life holds down the line. It is possible that I won't be there to protect one of them when they need it most and it's possible that they won't be able to protect themselves due to a situation I haven't planned for.
The moral conflict with the morning after pill would be on my shoulders and my shoulders alone. Why? Because if one of my young daughters was raped in a teotwawki situation, she would take something for the pain as she heals and something extra in addition to that and that is all she would know. I would probably not tell her she just took the morning after pill, depending on her age, especially if she's still very young. If she's older, say in her mid-teens, then this decision to give it to her without telling her becomes very tough and I can't honestly tell you what I would do at that point. Also, just because she takes one doesn't mean she just terminated a pregnancy. She might not have gotten pregnant from the rape. The pill would be a precaution against that.
If I'm wrong than I'll be the one to pay for that down the line when I'm judged, not her. I'm a father and it's my job to protect her. If I mess up on protecting her from a rape happening in the first place, then I can at least protect her from having to carry and deliver a rapist's baby at the possible cost of her own life. I'd rather burn in Hell for slipping her the morning after pill and having her continue to live than lose her during childbirth in a world where medical help is not available.
In closing, I'll be the bastard if I have to in order to protect my daughters. It's my job.