Yeah either way, it would hurt him. Charles was such a fighter and believed in Nassau so much I doubt he would just turn the other cheek. If he had lived to that point I think someone would have to kill him then to stop him. Can you imagine the rage he would have felt finding out that Woodes Rogers killed Blackbeard the way he did? He wouldn’t stop until he had Rogers head in his hands like he did with Ned Low.
Charles was a good man, as Jack said, but he was extremely persistent and the only way to stop him was to kill him. He got the ball rolling, so to say, by basically sacrificing himself for the pirates of Nassau. He wanted that war. His death wasn’t in vain, in my opinion and two of the people directly responsible for his death suffered greatly in the end.
I can go on all night but my point is that he would have sided with Flint and Madi because that’s what he died for in the first place – a rebellion in Nassau.