Could probably skip to the toddler phase and act like nothing happened, it did pass almost 3 months in game or so.
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The problem with that is:
1. It skips the naming phase, necessitating a redesign of the pregnancy system.
2. I would have to include a "meeting your kid for the first time" scene in the reuniting scene, which would be extremely clunky and awkward
3. I would have to account in all lead-up dialogue for the fact that MC wouldn't know for sure if he had a kid or not with that particular girl, or where the kid actually was
4. If a girl gave birth during the war, while MC was in a coma or presumed dead (some girls think he's dead, remember) they would almost certainly give the kid to Artifact for safe keeping, which would make it impossible to retrieve the kid as you wouldn't have named them.
All in all, it's much simpler to just have the MC say in Act Two: "I should wait until all my kids are born before I kick off this thing with the church. Who knows what might happen?" :)
Most of the side girls will be able to get pregnant in Act Two and probably Act Three as well once that point is reached.
That will happen when the game enters beta, though, and everyone will be strongly encouraged to start the game again once the beta period nears completion/gold release is done as the entire game will be getting a facelift and a code refurbishment just to make everything as shiny as possible before I declare it done :)