Following my own suggestion (second comment on the question), here's an answer which avoids the prompting altogether:
(let ((auto-answer '(("\\`Active processes exist; kill them and exit anyway\\? \\'" t))))
auto-answer.el, available at https://github.com/YoungFrog/auto-answer/blob/master/auto-answer.el (it requires dash.el from your favourite package store, and nadvice.el which is available at least in 24.4).
If you only want to avoid the prompt for some (specific) processes, the documented way to do it is to set its query-on-exit flag to
set-process-query-on-exit-flag when creating the process.