It isn’t currently possible to change the quality settings. Acorn will remember the last quality setting you’ve used though, so that might be an option for you (save an image as a JPEG with the quality setting you want, then run the automator action).
We’re also working on some batch stuff for a future release though, which will include what you’re after. To give it a good run though, we’re going to have it in private beta at first. Would you be interested in testing it out? Send us an email (email@example.com) if you think you would.