Your mystery flick is the 1987 TV movie
The Witching of Ben Wagner, starring Sam Bottoms, Sylvia Sidney, and Bettina Rae as the "witch". Full details can be found at YouTube, along with a clip that seems to cover at least a few of your plot points (including the rock-skipping scene). The plot summary: "When Ben Wagner's family moves to a small town, he makes a mysterious new friend, 13-year old Regina. Because Regina dresses differently than the other kids and lives with her grandmother by a lake, local gossip says she's a witch. When Regina tells Ben, "You can do it, Ben." Ben thinks she's put a spell on him and finds courage to do things he never imagined he could do. When Ben stops listening to gossip, he discovers that Regina's real power is her ability to get him to believe in himself. This enchanting story teaches that the real magic in life comes from helping each other believe in ourselves."