I don't think so. They would've had to drag out Neal's incarceration to six months or more, and that's a long haul. The investigation of the plane crash would probably be over, a lot of other stuff would've changed and moved on... it would've been too radical an interpolation in the planned storyline just to accommodate a real-life pregnancy that had nothing to do with what the writers intended for their show. Just because some shows find it feasible to incorporate actresses' pregnancies, that doesn't make it obligatory. In this case, it would've required too many alterations to the story plans, and for no valid reason.
And really, if they did decide to have Peter and Elle have a baby, that would've been the worst possible way to do it. Their whole process of deciding to start a family and getting pregnant happening off camera and then suddenly getting dumped on us as a fait accompli that happened months and months earlier? That's just not right, for something so big to be skipped over to such a great extent. If Thiessen had been only a month or two along at the start of filming for the season, then maybe they could've accommodated it in the storyline, but she was just too far along for it to be a good idea here.