There is only one thing that bothered me about your post: "3.) If a female is facing court-martial for pregnancy, might she cry 'rape'?"
For all women there is a significant stigma about coming forward about sexual assault. This is particularly true in the military, which has a very poor record of successfully prosecuting perpetrators. Sadly, my fear is that the point you raise could actually have the opposite effect of your concern: fear that this will be the response and they will not be believed may further inhibit women from coming forward if they have been raped.
Interesting point. I think there's truth to both sides of the argument, to be perfectly honest.
Next good point came from a poster known as TTC, who weighed in on the legal aspects of the ban.
The more I read about the policy, the more I realize the legal aspects of it. The media has used the term "court-martial" quite a bit, I think due to relative ignorance of the entire ins-and-outs of the Uniform Code of Military Justice. To be certain, pregnancy appears to fall under General Order #1, which bans--as TTC mentions--porn and alcohol. Violating any general order opens one's self to the possibility of court-martial, although it will probably go to the Article 15 level--meaning letters of reprimand, loss of rank and pay. Indeed, even punishment might be a bit of an idle threat, based on some of the convictions we've seen so far.