The smoking man (Old Alex.) knew this was going to happen.
The timeline isn't going to be rewritten into anything significantly different more so than last time this all played out, OR it's completely fixed, predetermined and can't change.
They made a point of saying that they don't know how time works.
From Keira's point of view however, if time doesn't play out exactly... Her kid might not be born.
There was an episode of journeyman where the guy from Rome, came back from the past to discover a future so completely different (he misplaced a camcorder) that just because he frakked his wife an hour later than he should have 9 years earlier, his son had been born his daughter.