In response to this Stack Overflow question Adding Color to Sankey Diagram in rCharts, I put this quick example together to demonstrate one way of handling.
Modified http://timelyportfolio.github.io/rCharts_d3_sankey//js/d3.v3.js to a secure url
Modified http://timelyportfolio.github.io/rCharts_d3_sankey//js/sankey.js to a secure url
https://timelyportfolio.github.io/rCharts_d3_sankey//js/d3.v3.js
https://timelyportfolio.github.io/rCharts_d3_sankey//js/sankey.js