While I think Cat was a little bit too vicious with his "post birth" version of the character, the player chose the problems associated with having a child. Assuming that her character would be able to be a Shadowrunner at 6-9 months pregnant is absurd. A player thinking ahead about consequences would have just created an interim character. It's not only foolish from a physical standpoint, but also from a psychological standpoint. Shadowrunning isn't exactly safe or gentle. It's an ongoing recipe for miscarriage. Only the most aloof and disinterested of mothers would continue any kind of "active" shadowrunning (and it sounds like she did since she was worried about buying new armor and reductions to physical stats). Even seemingly "harmless" activities like decking/hacking could endanger a fetus based on the amount of neurological shock the mother could incur. That character should have temporarily retired the second she found out she was pregnant unless the character was some kind of mentally disturbed individual. In fact, as a GM I would have explained that before I even okayed the idea. Fast forwarding a year to accommodate for pregnancy and then birth recovery just based on the choices made by a single player seems a bit unfair to everyone else unless you're playing in a campaign where time doesn't actually pass.
And if, fully understanding the impending consequences ahead of time she chose to go ahead, and assuming the player and GM agree that a female character having a child isn't an absurdly bad idea for a violent role playing game...
Don't punish the final character. If the player is willing to sit though the gestation period, they shouldn't be unduly punished. A woman who maintains an active lifestyle while pregnant and tries hard shouldn't have to try too hard to get their old physical capabilities back. If you look at contemporary female athletes (and celebrities with good personal trainers) who have kids, they bounce back quickly. Just because a lot of women dive into buckets of ice cream and plump up doesn't mean they all do. Active moms don't lose too much of their bodies. Maybe a short "recovery period" where their stats are reduced, but forcing the character to spend Karma to get back to normal seems punitive. Realistically, the character should probably stay retired through that period too, but maybe the player wants to get the character back in action. Shadowrunners shouldn't considered "typical". Giving an active runner (ie non-sedentary hacker, rigger etc) the benefit of the doubt seems fair. They are supposed to be above average after all.
Giving the character all sorts of arbitrary flaws like "Post Partum Depression" definitely isn't fair. We're talking about a mental disorder suffered by a small fraction of women. Again, shadorunners should be considered above average. The consequences should be fairly significant. After all, having kids is a huge change. Anybody who has gamed into their thirties knows how many players have been "lost" from the group or severely limited once they had a kid. For a shadowrunner, caring for a kid may well be the death blow to their career. What would have been fair to the player was suggesting that the character give the child up for adoption, or find a foster parent for it. It's a good way to explore the character's contacts, or even a way to bring their family or old friends into it. Might make an interesting side plot of sorts if you're really into roleplaying it. If they choose to keep the child, new flaws like "Dependent" are obviously appropriate. Lifestyle adjustments are obviously appropriate too.
The very fact that the player decided to retire the character after enduring the hardships of playing a pregnant character shows that you probably handled it too heavy-handed. While it's realistic to say that a Shadowmother would probably retire, and that's why I probably wouldn't allow it in my game unless the player absolutely insisted, it isn't very much fun. However, don't worry about Critias. He's not very pleasant a lot of the time.
