There's no real hard evidence to support anything, I'm afraid. But again I call the question of whether Guardia actually fell in the sense that they are no longer a power. There's evidence in the game to support the idea that Guardia "merely" suffered a massacre, and was able to rebound. Had the the royalty been killed, it is unlikely that they would be able to restore themselves to a level where they were even mentioned in the short 15(?) or so years that they were given.
So my assumption is either:
A. King Guardia was killed, but Crono and Marle lived.
B. King Guardia and Crono were killed, but Marle lived
C. Crono was killed (again), but King Guardia and Marle lived.
D. All of the above were killed, but they had a son => Unlikely, as even if Marle had been near the end of her pregnancy during the events of CT (which she couldn't have been, since she would need to be pregnant in the first place) the child would only have been able to be 5 (If I remember, the "fall" was 1005? Or was it 1007? If it was the latter than the child would be 7), which doesn't leave good odds for the kingdom.