In the Edit Citations, author Name settings, there is the comma, but as you no doubt discovered from the wording of your question, unless alll the authors are identical, it doesn’t omit the author et al and give you the “year, year” result.
Best bet is to exclude both the author and year for the 2009 citation and add the “, 2009” as the suffix.
I do wish Endnote would give the option to use the et al settings regardless of the remaining authors. It is so rare to have multiple authors exactly the same and in the same order!