Any advice about having children during grad school, from the perspective of (a) female grad students and (b) students without stay-at-home partners?
What you end up doing is going to be very specific to your individual circumstances, but I can give you my two cents about how my wife and I handled this situation.  Currently, I'm a 4th year PhD student and my wife is 2 years into a MS degree with the aim to get a PhD.  We both hope to stay in academia.  We have two kids, ages 4 and 6 mo.

Our first kid came before either of us were in grad school, and our second came a year later than we had planned. Our decision was to have kids earlier rather than later because grad school is more flexible in terms of schedules than real jobs.  This really helpful when my wife was practically bed-ridden for a couple months of her first trimester with our second kid.

We didn't want to stick our kids in daycare full time, and we have no family around to help, so we came up with a switch-off schedule.  My wife works from 4am-noon (and some hours on weekends) and then we switch off and I work noon-6pm.  Then I work at night from home after she goes to sleep (early).  Our 4 year old does go to pre-school a few hours a week and the baby naps, so I can put in a few more hours during the day this way.  Of course, schedules like this depend on our advisors being okay with our hours, and for our work (me CS, her biochemistry), it works out. Depending on where you are and at what point (and structure) of your MD-PhDs, you might be able to do this.

One consideration is that by the time both of us are on the job market for tenure-track positions, both kids will be school age, which allows us to both work normal business hours.  Also, by the time I'm into a post-doc, our baby should be sleeping through the night.  Until that happens, caring for children is very draining and it does affect my productivity in research.

As far as I know, my wife did not experience any overt discrimination against her for being pregnant.  Her supervisor was generally supportive and understanding even when she couldn't work because she was too sick.  However, as with many medical conditions (e.g. disability, known mental health issues), you're sure to encounter at least unconscious bias for being pregnant.