Is there a way to credit a customer's account in Craft Commerce?
Commerce does not, currently (= Dec 16) have any concept of a customer balance or a gift certificate.

You could do it as a plugin, I would think.  Basically you'd keep a list of emails and credits in a record (i.e. table) and then write a controller that you/the customer could call to apply those credits - the actual application of which you'd probably implement as a Commerce adjuster perhaps (https://craftcommerce.com/docs/adjusters).  

It would be a relatively involved plugin at this point.

In our case we chickened out on this, hoping it will come later to Commerce core - we just ask that the gift certificate customers call through their order.  Definitely not ideal but for the relatively few GC customers it didn't seem worth the development effort.   Gift certificates are an often requested feature for Commerce, though, so you'd expect it to happen at some point.

Vote here for the feature - https://github.com/craftcms/commerce/issues/253