User blog comment:Morganaforever/Episode Review: The Hollow Queen/@comment-4892425-20121125020228/@comment-5674726-20121125100732

Talk about a monkey wrench - a legitimate heir or heiress to the throne that would cancel out all Morgana's flimsy claims to the crown.

I can't see it worsening her position.

Even if, under other circumstances, Morgana might be entitled to be heiress presumptive, until Arthur had a child of his own - as would appear to be the case based on Gaius' words in The Crystal Cave - I would imagine that she's considered to have forfeited any succession rights she would have had.

Both times she took the throne, it was by right of conquest, apparently legalised (somewhat?) because of her Pendragon blood. Once she no longer has Guinevere to either rule as her puppet or obligingly surrender the throne to her, I imagine that Morgana will plan to conquer Camelot again. A baby isn't going to be an obstacle for her, not compared to the trouble its parents can cause, and it's potentially an asset to her if she has the good sense to (a) secure it as a hostage during her takeover, and (b) raise it as her successor.