For instance, play on my headphones will launch iTunes. If I disable com.apple.rcd, the controls stop working altogether, which leads me to believe the change needs to take place around rcd. Are there any workable solutions for this, or third party tools? I would essentially want to remap the RCD inputs to the match the media keys on the Mac (or others if necessary).
There is a patch for rcd, I found it in an answer to another question. http://lifehacker.com/5651055/free-your-macs-media-keys-from-itunes-no-manual-hacking-required
It patches rcd to not launch iTunes, and instead use what ever program is open. I use it to control VLC without having iTunes launching if I forget to open VLC first.
It does not seem to fix input from bluetooth headsets however, if you want to use those to control audio you will have to work harder.