Were they allowed to have the word "rape" or even "sex" in any nintendo or super nintendo games?
as far as outside of Japan, no. Games like Final Fight had censored under-cleavage and various other changes just for the western audiences. However, games inside Japan themselves had sex and sexual themes for sure. I know that Lennus II has sex in it.
As far as the Chrono world goes, I don't think they really had classes. The one 'outsider' that we know of in the guardian mating history was Leene, and she was a villager/peasant/whatever of the commonplace. Furthermore, I don't think there are any mentions of suitors for Marle in the game at all.
If there isn't a policy for suitors/royalty for the royalty, then a person kidnapping the heir to the throne and threatening to sire the next heir could be foreseen as an act to overthrow the kingdom.
One last thing I'd like to bring up for consideration. Do we know when Yahkra took over the Chancellor in Crono's time? He did use a trial to overthrow the kingdom via the rainbow shell, and perhaps Crono's trial was his first attempt? If that's so, a prosecution charging rape with the notion of overthrowing the kingdom might be a sufficient scheme for Yahka's revenge.