This does sound like a good idea and we'll definitely have a discussion about this, although I wouldn't be able to give a timescale on when such a feature could be introduced.
There is a possible workaround you can use using our new PDF themes generator.
Using the ability to customise the HTML and CSS on the PDF themes you can insert an additional image (i.e. a take online payment button) which links to your payment gateway, this isn't ideal though as the invoices won't be marked as paid in KashFlow.
More information on that is available at http://www.kashflow.com/developers/pdf-themes/