Nice work Kyle. I concur, this workaround works for now. Go to Sales > Invoices, click an invoice and then from the More Actions menu on the right, choose Print and the (annoying, stupid, invasive, call it what you will) Pay Invoice button does not appear.

I think I have normally been making the invoice and then using the actions in the footer of the invoice (before closing it) to print the invoice and this resulted in the button appearing on the PDF.