There is currently no way to set a default for this option. We will however add this to our to-do list.
You can use the following SQL to set the option to use HTML format for all existing users.
SET pluginvalue = REPLACE(pluginvalue, '<UseHtmlFormat>false</UseHtmlFormat>', '<UseHtmlFormat>true</UseHtmlFormat>')
WHERE pluginname = 'Email'
Shutdown the Continua CI Server service before making any updates to the database. Changes will be picked up when the server is restarted. Also ensure that you have an up-to-date database backup in case anything goes wrong.