And there it is. One of the central themes of the entire Water 7 and Enies Lobby arc.
There’s nothing good, and nothing bad in building a ship. That is to say, there is nothing good or bad about something existing. existing is not a crime. Tt is truly, and wholly, neutral.
Franky and Tom are in the same situation. They both built a ship/ships that were used to commit crime. And they are not at fault for that, and they certainly don’t deserve the punishment they get. But. They still have a responsibility towards those ships.
And that’s the other big theme of this arc: responsibility. Specifically, responsibility for one’s choices.
Franky and Tom both chose to build those ships, and so, they have a responsibility towards them, as creators.
They, and Iceburg, also chose to protect and keep the blueprints to Pluton, and so they are responsible for those as well, to keep them safe as they deem necessary.
Usopp chose the Merry over the crew, and so he’s responsible for the consequences of that, both good (the Merry saving the crew at Enies Lobby) and bad (leaving the crew). And that’s why Zoro demands an apology, because he wants Usopp to take responsibility for his choice.
And Robin. She chose to learn the forbidden knowledge, and so she’s responsible for that knowledge and what she does with it. For her, that means continuing her research for those she’s lost. And she also upholds a responsibility to the world’s safety, in regards to the ancient weapons, when she refuses to give up Pluton’s location to Crocodile, until she is forced to abandon it. Because she also chose to join the Straw Hat Pirates, and she feels responsible for their safety, and she chooses to uphold that above all else. And it is her choice to live that is the main catalyst of Enies Lobby’s conclusion.
None of these choices are necessarily good or bad. The narrative doesn’t judge these choices on a moral scale. But it does say this: once you make a choice, you are responsible for the consequences of that choice.
It makes sense that this is the first time that Luffy’s captaincy is seriously challenged. Because as captain, he has a responsibility to his crew. And that comes back in a big way in Sabaody, and the foundation for that was laid out here.
TLDR; Franky’s backstory encapsulates the two major themes of this arc: existing is not a crime, and responsibility for one’s choices, and also I love it a lot.