You might try to create a field with a formula to calculate the current date / time of a workflow run. Then check the "Group Data Into Separate Reports" option in the Render Tool's configuration, select the current time stamp field in the "Field to Group On" dropdown, and select prepend or append the group to file name in the dropdown underneath.
Use the "Date Time Now" tool, and set the format to "yyyy-MM-dd hh:mm:ss". I would also convert it to a string and do a Replace formula to remove or replace the "- / :" symbols to get to a more standard file name.
It should still only create a single excel file per run, but appending the run time and date will keep it from saving over prior exports. You will still have to clean up the old files manually unless you automate it separately.
