Is there a captcha plugin that does work with jetpack? Forget Akismet….
Jetpack Comments is not be compatible with Captcha plugins like BWS captcha. Since the Jetpack comment form is hosted on WordPress.com and added to your site via an iFrame, Captcha plugins can't hook into that comment form at the moment.
Akismet, however, can be used with Jetpack Comments, and will filter all comments submitted through the Jetpack comment form.
If you want to use Jetpack but prefer to keep using the BWS captcha plugin, you can deactivate the Jetpack Comments module by following the instructions here:
http://jetpack.me/support/#turn-off-jetpack-modules