*puts my historian hat on* I think that Thomas Hamilton was doing the absolute best he could have done given the shitty situation he’d had handed to him. It was not within his power to just hand the island back to the native peoples there, so he was attempting to help the people there the only way he could – to pardon every last one of them, and given that they were a conglomeration of all different ethnicities, religions, and creeds, I’d say that all of them definitely did not refer to just white pirates. His eventual goal may have been proving that the people of Nassau could self-govern. In trying to push through the pardons, Thomas was trying to change the way that England viewed the poor – he was trying to get the nobility to see that granted a chance, the people of Nassau would prove to want to be productive, law-abiding citizens of the Empire, not criminals, thus disproving the idea that the nobles had that the poor were born criminals by nature. it was kind of a thing at the time – strict social stratification of the sort that’s become ingrained in English society over the past several centuries had begun to exist, and England had also adopted a really rigid criminal code where the punishment for a lot of things was death. If you want a good book on the subject, I can recommend The Thieves’ Opera by Lucy Moore.
Anyway – long story short – no, I do not think Thomas was talking about just pardoning white pirates. I think, as James noted at least twice, Thomas wanted an end of British rule in the West Indies, or at least an end of tyranny. I think he would have supported the notion of the people of Nassau ruling themselves – James specifically said in s4 that the victory he felt was impending in Nassau was one that Thomas had given his life for, meaning that they shared that goal.