Sister Claire/WMG

Claire is the daughter of a witch.
A silly WMG, but Claire adores cats, feels that playing with that one white kitty feels so right, It'd be a nice twist for the new Mary to be of the very bloodline that started the whole war on God.

Gabrielle is not quite an angel...
She is a Fallen Angel. The company G.O.D.? Well, Lucifer did want to run the show... Also, arn't some demons described as looking like angels? Gabrielle's visits tend to get Claire into a lot more trouble than she'd normally get into. Also, the fish-people (merpeople?) seemed to be more devilish or fae than anything 'nice'... Also, how many 'names' does Gabrielle go by? The only angel I know of who has many names is a certain Fallen. Which would mean that...

Claire is pregnant with an antichrist.
See: Gabrielle is not quite an angel. Now, first things first: "The Antichrist" is not Damien. An antichrist is pretty much a person that says they're a Christian but doesn't believe Christ is God. Following the other "route", the child would be false prophet that would screw up people's faith in God. The later would help The former, not so much. The misconception... yes.

Catharine is Claire's biological mother, and got pregnant with her in the same way Claire got pregnant.
There's been foreshadowing and hinting all over the place for the former, but the later would help explain why she, a nun, would have gotten pregnant. It would also create some interesting mirroring between their stories.
 * In a similar vein, her nickname for Claire is another hint. In another life, Claire's name was probably intended to be Clementine. This reasoning would explain why the Evil Cat always refers to her as Clementine. That's what Catherine sees her as inside.

The Reverend Mother knows about Claire's pregnancy.
I doubt that none of the other nuns have noticed things, and the RM has shown a lot of interest in Claire since the whole Sister Cat thing. Maybe she has access to a prophecy or such that lets her know Claire's preggers with the Messiah, but hasn't shared it with the other nuns for the same reason that Gabrielle warned Claire not to tell any of the other nuns.