I wrapped my pen with the same barriers that I use on light handles, switches & chair adjustment knobs. I also disinfected the pen after the procedure. If your barrier tape is to tacky and difficult to remove quickly, you can fold a part of the barrier over itself so that you have a piece to grab onto and the rest will peel off more easily.
It may also be a good idea to rest the chart on a counter or bracket table that you know is clean and to use a pt. bib or paper towel to cover the part of the chart that you're not writing on to prevent your hand and wrist from contaminating the chart.
Sometimes I ask the pt to do me a favor and chart perio for me. Explain the process and the odontogram before you start. When you call out probing depths, bleeding, pus, recession, missing teeth, furca, etc, they are hearing it and also physically writing it down. I feel that this can be helpful for education and reinforcement. When you summarize your findings after charting, the pt. will have a better understanding of his own disease state and potentially enhance pt. compliance.