It looks like each time the plot is redrawn a new plot object is appended to the <div> element. Is there a way to fix that behavior where the newly generated plot object replaces the already existing one?

Sure! What Plot returns is a "standard" DOM node. It's possible to empty the #container before appending it, or select the previous node and use https://developer.mozilla.org/en-US/docs/Web/API/Element/replaceWith.