Well, yeah. Of course you disagree, you've already shared how you handled it and that made your idea pretty clear. I tried to be pretty brief and explain why I felt the way I did, but since that apparently didn't make my point clearly enough, that's fine; I'll go a little more long-winded, too.
I'm not saying you're wrong or that you should be strung up, I just said that's not how I'd handle it. The difference between magic loss for cybernetics or deadly wounds is that there are already rules for those; these are things you made up, then shoved down the character's throat because they'd "thumbed their nose" at you. The fact that your other players cheered and clapped doesn't change that fact, to me. Likewise, the experience of the one other female player doesn't mean these aren't necessarily realistic; I know women who've trucked along just fine through the vast majority of a pregnancy.
But the thing that cinches it for me? Whenever you outright say "she was not happy," and "she wanted her character as she had made it, not this one..." it tells me maybe you should stop and re-evaluate your GMing style. I'm as big a fan as the next guy of challenging players. Hell, just ask some of my players. But there's a difference between challening them, and making them outright "not happy," and offering them no alternative but to retire a character for several sessions or make a new character outright.
"Flaw: Cannot get up unassisted, Flaw: Damage Check for Child on a Fall, Flaw: Larger Target, Flaw: Mood Swings, Flaw: Tires Easily, Advantage: Shown Mercy" are all stereotypes of pregnant women, sure, but they're things that are pretty damned arbitrary to fling on a character who already was "not happy" the last time you'd tampered with their sheet. How exactly does Mood Swings work? What's the difference between Tires Easily and the Asthma negative quality? How does "Larger Target" work (and why doesn't every Ork and Troll in the game already have it)? Why does she have to check for damage on the baby when she falls, but not when she gets shot? What counts as "assisted" for standing up (what Strength score is required), and why doesn't someone with a very high Body and a very low Strength get the same thing? How exactly does "Shown Mercy" work, and why is it a universal truth in your game world that every NPC will react to a pregnant woman in the same way?
Tacking on outright attribute penalties (that are pretty crippling), and all I see is a GM that's getting cheered on by the other players, while punishing someone who wanted to role play adding some depth to their character...you gave them remarkably tangible drawbacks for no tangible benefit, because they "thumbed their nose" at you and everyone else at the table was clapping.
This is all -- in my opinion -- a lot of bookkeeping, a lot of house ruling, and a lot of punishment. It's neater and easier to just adjust Lifestyle costs (the default "you're eating more" alteration, maybe even as much as a Suprathyroid Gland's drawback), and then gloss over the most physically incapacitating trimester. I'd fast forward over those several months for all my players -- give everyone some training time, 3d6 x 1000 nuyen and 2d6 karma to cover "pick up jobs," and call it a day. Keep the Lifestyle adjustment after the baby's born (a new mouth to feed), look into a Dependent Flaw balanced by a Will To Live or Guts or something (to show a newfound, parental, willpower and determination) ...and game on.
No hurt feelings, a player is encouraged to RP rather than discouraged, and I never have to type "she was not happy." Everyone has fun, everyone gets a little down-time for Initiation or a trip to the Beta clinic or whatever, etc, etc. It might not be as funny a story to tell on the internet to try and impress the other GMs, but I'd rather that my players enjoy my game than folks on an internet forum.
Compare my end results to yours -- a retired character because the GM fucked it so hard, and another PC stuck throwing money away after every run -- and ask which game you'd probably rather be in? Heck, I'm surprised that player hasn't posted about this in "Gaming horror stories," to be honest.
We complain over in Off-Topic about gamers having a bad rap, or about there not being enough female gamers...how would you guys like it if the shoe was on the other foot? If your swaggering go-ganger just wrapped up a big job and had some money to spend, how would you like it if you laughingly scratched a thousand nuyen off your sheet (instead of carefully and meticulously spending every single dollar you earn, ever, on being a more lethal character) and said "Oh, and he goes and gets laid!" and then the GM started to scribble all over your character sheet due to a debilitating STD? Would it be as funny if it was your PC that got their stats lowered, their karma spent for them, and a slew of new Negative Qualities?
GMs moan and cry about characters only wanting to roll-play, and not role-play, but then a couple PCs engage in a romance and this is what they get for their trouble? Really? This is commendable?
But failing all that? Why not tell her the in-game results of a pregnancy before you write up a new character sheet and make her run it (and then before you do that again, and before you do that again)? Why ambush her with it like you did, if -- deep down, really -- you weren't out to punish her?
You even said you asked what their intentions were before you "acted accordingly," so why not have another conversation with them and lay out exactly how gimped the character would be? Instead you blindsided her with it, and did so so harshly she retired the character. How did your campaign benefit as a result, except by nipping an inter-PC romance in the bud and taking some depth away from the group of player characters?
Those of you high-fiving him and clapping him on the back, here in this thread...ask yourselves, really, how did driving this character away, and making a PC miserable, make the game better?