Yes, there is a very simple way to get audio out through the iPad headphone jack even while connected to HDMI to play movies on a projector or TV. In fact, I just did it last night for a presentation.
With the HDMI adapter connected to the projector and your audio jack plugged into your iPad headphone jack, go ahead and start the movie. Then simply unplug the headphone jack and plug it back in. The audio is now routed through the headphone jack again.
I found I only had to do this once per session. That is, Iwas able to stop the movie, go to the beginning of my presentation, wait the 20 minutes for the meeting to begin, and when I got to the video clip the audio still played out through the headphone jack to the PA system.
I had built a presentation in a Web oriented training tool and it was running on Safari iOS7 with the latest update. I have not tried it with Keynote yet.
iPad mini (original version)