I think more about how B'Elanna was practically in labor (and then finally IN labor) during Endgame when they were like...in the midst of their final battle.
But yeah, other than THAT, I never had an issue with it and I don't think they even considered abortion. After all, Naomi Wildman was born on that ship and she loved it, called it home...all that good stuff. I think B'Elanna and Tom were surprised, but even though they weren't planning on it, I don't think aborting was really an option for them.
Just because the ship was in danger a lot, the kids seemed to always survive and most of the crew survived. It's not like the baby would be going on any away missions!