Alex,
Currently we have two websites using the same MySql server, separate DB's, as a backend. I couldn't find a way, other than what I previously suggested, to have a separate binlog for each database on that server. As far as I can tell both are forced to use the same binlog. My initial goal was to have a seperate physical binlog file for each database.
I'm curious if you have an answer but I'll probably go with my solution because it offers other benefits like separate logging/data directories and files, separate user accounts, etc and the ability to start and stop without disrupting other websites. It will be easier to analyze the logs since I won't have to determine which db is creating the activity.