You isolate the code you want to obfuscate in a jar, and put it with the source code for the Cordova plugin you're creating (under src).
Then you mention the jar in the plugin.xml file with <lib-file src="src/path_to_jar"/> so that Cordova knows it should treat the file as library when packaging the code.
This is how the mpay developers did it. They put the jar here and mentioned it here.