While I agree that Scrubs, like most Hollywood productions, ended with its characters choosing not to abort, I can't agree with you that it was "typical" of such productions:
1. The show has fairly consistently portrayed JD as something of a man-child who refuses to grow up. This episode, consistent with that, showed him knowing what the right thing to do was - the responsible, adult thing to do - but looking for excuses to avoid it. Note that that antis in his pro- and anti-child list are almost uniformly ridiculous.
2. It was also fairly clear in the show that JD was not listening to "Jesus" not because He was irrelevant, but because He was not saying what he wanted to hear. Again, he knows the right choice, but doesn't want to face up to it.
3. Jordan told her son about her abortion - inducing him to run around the hospital screaming "Mommy had an abortion!" - because having an abortion is a pretty mortifying event that no one talks about.
4. Also, re: Jordan, she told JD and his girlfriend that she had an abortion when she was 19 because having the child would have ruined her life. At 19, she was a pitiful, drunken slattern. Now, pushing or past 40, the character is . . . a pitiful, drunken slattern. The story, to me, seemed a backhanded endorsement of the pro-choice position at best.
5. Most importantly, the story was not a "What is the mom going to do?" plot ending with what we normally see, a stirring declaration by the mother that the choice is hers, and she, and no one else, is choosing to give birth. Instead, JD and his girlfriend discuss the pregnancy together - it is clearly THEIR issue, not just hers. And the show does not end with the standard "Oh, I'm choosing" fare - the characters see the baby - see that their friend has grown up - and know that being responsible grown-ups is the right choice.
I understand how you see the show the way that you did. I was not that thrilled with the episode, mostly because it wasn't that funny, but I was certainly surprised to see the tack that the creators took. I don't think it was as negative (or "standard") as you seem to imply.
