Go in after and use a wave editor to reduce the gain on the slaps. You can play around with the volume until you get them to the right level. Little time consuming, but probably the best way to do it if you want to keep the natural feel of the playing.
Also, how are you micing it? If you're micing anywhere near the body, that would be the first thing I would change. Is this a solo acoustic? Does it sit in a dense mix? What? Playing around with the micing would probably help out a lot, as long as you're not set on the micing technique you're currently using.