Can I subscribe someone in Salesforce and apply a coupon?

Yes, if you are adding a subscription in Salesforce, you will be able to apply a coupon, as well. 

Please make sure you follow these steps when adding a subscription via SFDC:

1) From a record in the Recurly Accounts custom object in Salesforce, click "New Recurly Subscription": 


2) You will be presented with a custom Visual Force page that will allow you to enter Plan details, amount, add-ons, coupon discounts and dates just as you would within the Recurly UI.