There was a message at the bottom of this page that Intel will repair or replace the product under standard warranty process:
Option 2: Replace the Intel Compute Stick under warranty
If you choose not to use the App Update, Intel will repair or replace affected product under the standard warranty process. To obtain warranty replacement, submit an Online Service Request.
I submitted a ticket last night and am waiting for their response.
Now this aside, is there anyway to perform a clean install of Windows 8.1 on the stick?
You should receive the replacement Intel® Compute Stick with Windows® 8.1 installed on it.