I think they cut the baby storyline short because they found out Kelly Ripa was pregnant in real life and they didn't want 2 pregnancy storylines.
I have mixed feelings about it. I would have only wanted the baby to born if it was Ryan's. But it would have been nice to have Gillian have a baby because when she left there would have been a part of her still on the show. One of my biggest pet peeves is how they acted like Gillian never existed