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So from the Lucky episode if Ethan can be believed it was Amerlia's idea to betray Blackwell to the witchhunters. In fact it could be said that Amelia was more at fault because she manipulated Ethan with the whole "written in the stars" in order to get him (Ethan) to give the sway to Eben to use against Blackwell. She obviously made it seem that they could be together once if Blackwel was out of the picture. Hence why she neglected to tell Ethan that the for the Blakes and Connaughts written in the stars is also a curse.
We know from what Jake's mum said in episode 11 Witness that Amelia was devasted by John's betryal hence why she wasn't on the boat. And we all know that hell hath no fury like a woman scorned, as the her ultimate act of revenge was to arrange his death and be rid of his evil. The reason she never spoke about Blackwell to Cassie is because she probably didn't want to acknowledge her role in his supposed demise.
If Amelia did instigate what happened that day then she was partly responsible for what happened the resuting deaths of those who lost their parents. It would also stand to reason why Charles chose to extract his revenge by killing her in a fire in her house. If she was to blame for him losing his spouse in the boat fire then perhaps that is why he chose to kill her in the same way. As a bonus he gets to ensure that Cassie has to come to Chance Harbour so that Dawn and him can use the circle in order to regain their own powers.
It will be interesting to see how Charles ineracts with Blackwell once he learns that he's alive and back in Chance HArbour. If memory serves Jake's mum said that Charles and Dawn were up on deck with Blackwell, which leads me to believe that Charles and Dawn were definietly on John side.