Actually, Alex's story line has always been linked to taking care of Supergirl. The only time there was the disconnect was when she couldn't remember she was Supergirl's sister.
I rewatched the season premiere yesterday and was struck at how tightly Alex's job was still connected to taking care of her little sister. Even with her new lover at her side, all Alex could do during Lena's introduction at the Pulitzer party was watch how Kara was taking the seemingly subtle hits then praise from their billionaire friend.
During the ensuing fight, DEO director Danvers did surface to direct Jonn to lead the villlain away from the party as everyone else followed to do battle. And far from barking... she did provide some much needed levity when she arrived to fight in an evening dress while Kara, Brainy and Guardian had not only beat her to the auditorium but also found the time to get dressed for the fight.
As for supposedly dropping the whole baby storyline, Kelly already knows about Alex's secret desire since she backed up Alex during the possible adoption story last season, but now that these two are a new couple they need to see how well they fit together before introducing an new destablizing force like a baby.