Just looking at Neo's state when freed from his pod, I doubt that bluepills still in their pods would be able to successfully carry babies, as it would be far less efficient than harvesting eggs and sperm and growing the child in their own pod (which would act like an artificial womb). It doesn't make sense for the machines to possess the technology to hack human brains directly, yet be unable to surgically remove their reproductive materials.
Intercourse in the Matrix would NOT make someone pregnant in the Real - there's simply a lack of needed genetic information being exchanged. Just because you have access to a digital form of the data does not mean that your body can replicate something it could never naturally produce in the first place - two "Real" people are needed to have a "Real" child.
My guess is that normally, when a couple conceives a child in the Matrix, the machines harvest their genetic material from their pods and create a child, which is then "born" to them in the Matrix. This would account for the facts that people's RSIs look like themselves, and children look like their parents - the child's genetic information MUST come from the two parents (barring extraordinary cases where the Machines get the process mixed up and the 'wrong' child is born with a different identity - which I believe happened in one of the comics).
In the case of redpill parents, if one has an absolute belief in being pregnant, without the ability to 'donate' genetic material to the Machines, it is possible that the System might do what it does best, and adapt to account for the inconsistency - in this case, a child would be digitally created from the material of the parents, yet would not have a corresponding form in the Real - in essence, the child would be a Machine program created with the purpose of keeping the System running smoothly. This is, however, a bit of a stretch, as it would be far more efficient simply to simulate a failed pregnancy even in the most extreme cases - and usually simply to convince the 'mother' that they are not pregnant at all - not all intercourse results in pregnancy, after all.
The best way for redpills to become pregnant would be to have real sex with your real partner, in the Real.
... And now I'm stuck picturing Keanu Reeves' naked backside during that 'Rave' scene.
... And now you all are, too. };->
- Void