I wouldn't suggest making your own resource files. Many players like to use mods that have their own resource/config files, like FDF, ECP, etc. Making your campaign have one might frustrate some players, since they might not be able to use those mods.
Also, there is no way to ensure that your 'mod' is running when a user plays your campaign... since you can't include campaigns in mod folders.
On the second Q though: does anyone know how exit.sqs works? In the com ref it says that this script is run after the mission exits, so perhaps you could use one to 'override' the default island cutscenes. I've never been able to get the thing to work though, so I have no idea what/how it works.