Now that I have access to my SDK VM and the N900, I've fixed up the patch and merged it into the repository:

http://repo.or.cz/w/headphoned.git/c...ff/3077ae9b0fc

It works fine for me during testing with Skype's echo123 lady, and I assume it works also for incoming ("ringing") calls. It did not work when I sent the "pause" signal immediately when the call was disconnected, so I now send it 500ms after the call has been disconnected. It works reliable now for me, but you can hear ~ 400ms worth of your music between the time the call is disconnected and the time the signal is sent by headphoned and processed by the media player. Still better than pausing it manually in my opinion (although I can anticipate some bug reports complaining about this behaviour.. hehe).

This feature will be part of the upcoming headphoned release. Thanks for your valuable input, Surstroemming and Faheem