if so browse all the other rcX.d folder and check whether your mysql is run there. I had around 3 files in rc2.d folder.
all of which are symlinks...
rcX.d folders contains most start up daemons and are on different run levels if you know what run-level your mysql is starting up with. then go to the corresponding rcN.d folder. I hope this helps. Although I would do the same as Dickey when I want to temporarily disable mysql. If you are running a different flavor of linux can you post here what dist. you are using?