Well, what with Tom being arrested for 'building the Pirate King's ship', who else thinks that Kaya will be arrested for giving the Straw Hats their first ship? After all, it's inevitable that Luffy will become Pirate King.
Then again, there may not even be a WG when Luffy's king, plus the only ones that know Kaya gave them the ship are Kaya and the Strawhats themselves.
You know, considering the story line, this could be another reason why the Going Merry was replaced. Think about it, if Kaya gave the Pirate King his ship, she really could get in trouble for it.
However, having their ship be replaced and built by another future crewmate fixes that. Now the blame will be on Franky, since I doubt the WG will remember the Going Merry after the SHs reach Raftel with their new boat.