I am not necessarily having Inkskin kill herself when defeated at Tidewater Rock. If the PCs kill her themselves by reducing her to negative constitution, I'll proceed with the game as written and he'll probably just be an "unsolved mystery".
If she survives and is taken prisoner, I'm going to spin the story that Cyrus Wolfe is not hundreds of years ago, but just a generation ago. Wolfe would've had Inkskin's father as a first mate and Inkskin will have been a child along with him on the ship. Wolfe will have killed Inkskin's father after cacheing his treasure at Mancatcher Cove to remove witnesses and then will have sold Inkskin to Soshimira to be rid of her.
The rest of her story will proceed as written. However, Inkskin sees working for Kreloort as trading one master for another and wants to be free of all of them. If revived and questioned, she'll try to convince the PCs to take the treasure of the Cove which she knows is there in hopes they'll kill Kreloort and free her. She is going to hold back the knowledge of the Canopy Creeper to use as a bargaining chip for the PCs to free her and allow her to return to the Thresher (which will be hiding in the Cover as written) to use it in aiding them if they become desperate during that fight.
If they do so, she will hold the Cove with her ship and the PC's ship while they explore the cave. The ancient mariner is going to be the remains of her father and I will move her ruined music box from Kreloort's throne room to the mariner's possession. If the PCs present the music box to her, she will become a friend (although a thoroughly evil, uncontrollable one) and will pledge her ship to their fleet in the final chapter.
For me I'm keeping him in reserve to tie in with backstory. We're starting this AP in the new year, and one of the opportunities I gave my players was to come up with any object at all and say that they had it in their possession when they got poisoned. The object is definitely gone when they wake up aboard the Wormwood, and what it was and what happened to it will be something I figure out once I see what they each create. I'm hoping that the Ancient Mariner can get drawn in that way, so that he feels like an organic part of someone's backstory.
I had him wearing a cursed amulet that is slowly turning the party wizard into an undead version of the mariner! It has been awesomely fun so far!