I agree that this sounds excessive for an EDF. While I am careful about making sure I let them know about early departure when I check in, it certainly makes no sense for them to charge for an entire night. The room is returned to inventory and available for resale. There are also no ancillary costs associated with the empty room (maid service for that day, towels, etc).
That being said, if they were going to charge for a full night it absolutely should have been on the portfolio. I would send a copy to the credit card company, along with a letter explaining the desk clerk assured you there would be no problem checking out early.