Every 'artifact' that gets generated needs to have it's own rebel.xml file associated with it. If you look at the contents of rebel.xml it simply points to where JRebel can find the source directories, and these are generated to absolute paths by the maven plugin for ease of use.
I would be sure to put the JRebel plugin in a separate profile that is only active on development machines so you don't get these files generated for production.
For the ear, you don't need to remove the plugin. I don't think it will hurt anything, you just wont get much benefit from it. JRebel will find the rebel.xml files for all the separate jars/wars and use those as needed.
So in short, you are adding them in the correct spots.