Poison him after he abdicate, surely? Move the blame away from himself - Why would he need to KO his father when Daddy is already safely setting up home with Stepmother Mary in Scalloway Castle when he eats some dodgy shellfish and dies. Ooops. But Charlie isn't able to be blamed.
Well, an abdication hurts the prestige of the monarchy, removing James before he gets the chance to be pushed out, removes a big potential mess, and Charles doesn't need to be tied to it, someone else could do the deed.
Also, if CHarles is alive, alongside another brother, I don't think James would marry Mary. She wanted to be a nun otl, and only married James to bring about a Catholic dynasty.