Although I have set the minimum order in system > configuration > sales, it does not prevent the customer from ordering with the "Check out with Paypal" button. Is there anyway to include this checkout option in the minimum rule?
You need to change the scope of the minimum amount setting. For that you need a new module with a
system.xml file that contains the same path to the minimum amount field and just changes the
Complete explanation can be found here: https://magento.stackexchange.com/a/9855/146