Is there a utility to rename payees AFTER they've been downloaded?

sgtempe

If not, what is a good way to handle this?

splasher

The renaming rules will only help in the future. 

There is an edit & replace capability in register.  Just select the transactions you want to change using standard Windows selection methods and then right click on that selection and select edit from the dropdown menu.

Try it with a single transaction to get the feel of how to do it first.