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