She wasn't conclusively one of the people stated in the prophecy yet; she was basically the expected person, but she hadn't engaged in any actions from the prophecy as of yet, so there could have been some wiggle room for nudging her out of the role by killing her, knocking things off track.
I don't think it's directly stated in the novels, but, as I recall, it's because Ce'nedra hasn't yet enacted any specific action that ties her down as being the named person in the Prophecy. At this point, she's only referenced by virtue of title and heritage, not by any specific action she's engaged in.
When she first gives the speeches to build her army, she's referred to; she's now Garion's fiance, and thus the 'Bride of Light' (and eventually 'Queen of the World.')
"How could you possibly-"
"Certain events don't just happen, Ce'Nedra. Some things have been implicit in this world since the moment it was made. What happened today was one of those things." She reached over and picked up an age darkened scroll from the table. "Would you like to hear what the Prophecy says about you?"
Ce'Nedra felt a sudden chill.
Polgara ran her eyes down the crackling parchment. "Here it is," she said, lifting the scroll into the candlelight. " 'And the voice of the Bride of Light shall be heard in the kingdoms of the world,' " she read, " 'and her words shall be as a fire in dry grass, that the multitudes shall rise up to go forth under the blaze of her banner."
She's now engaged in actions named in the prophecy, in her named role. But, up until then, there was nothing conclusive that said she HAD to be the right one; if she died, Garion would have ended up with a much younger (than himself) bride some time in the future, delaying the process quite a bit, or (Cthuchik hoped) derailing it altogether, since the other companions might not survive that long.
From Enchanter's End Game:
The word determines the event. The word puts limits on the event and shapes it. Without the word, the event is merely a random happening. That's the whole purpose of what you call prophecy - to separate the significant from the random.
All of the other members of the party had already engaged in actions that clearly tied them to their named roles, Barak was already the Dreadful Bear, and so forth. (Even Durnik was safe, although we haven't necessarily been told everything that the prophecy says about him. What we DO know, however, is that he was going to 'Live Twice', so killing him could simply cement him into his role -- whereas Ce'nedra's only protection was being the only eligible person for her role in the current generation.)
All that being said.. He knew he couldn't kill any of the others, because they were identified (by past actions) as the companions named in the prophecy, and had defined actions still to do; he knew if he tried to kill them, it would fail, as neither side of the prophecy would allow it to be invalidated until the final choice. But Ce'nedra wasn't positively nailed down yet by her actions, and was the one vulnerable person.
"One of the others will do just as well," Ctuchik asserted, his eyes blazing with fury.
"No," Belgarath disagreed. "The others are all unassailable. Ce'Nedra's the only vulnerable one, and she's at Prolgu - under the protection of UL himself. You can attempt that if you'd like, but I wouldn't really advise it."