Gareth,I agree that the red flag flew at all these places, but as part of the official assemblage of the navy. That's not the same thing as saying that "Red is the colour of the new republic!" to say that you were trying to create a "new republic" would be immediately recognizable as treason--not just mutiny--for a British officer in the nineteenth century. To claim that you were "waiting for the revolution" and "waiting for Bonaparte" would be similar offenses.
The Hermione did revolt at sea. But that revolt was not a well-defined political action with republican leanings. It bears no resemblance to the ideals protrayed in the song. So I still don't think any of these mutinies can credibly be the basis of the song. You have to be really eager to see a connection, otherwise, the parallels are not at all close.
(BTW I recommend Dudley Pope's history The Black Ship, recently republished in the Heart of Oak Sea Classics series, as a source on the Hermione affair. This is not one of his novels, but a historical account.)
Nerd