I am also frustrated by this update. I have found a work around I think.
1) Create an invoice like normal
2) once complete save and close the invoice creation screen
3) exit the invoice creation screen
4) toggle to Sales:Invoice and locate your invoice.
5) It looks like if you send the invoice from here it doesn't have a "pay invoice" button (I'm using the "Old" invoice layout)
I print all my invoices and if I print from there it doesn't have the button.
hope that helps
Kyle
