Separation in both these software does not mean the Apple is getting rid of the software. They will be seperated only for Podcasts this will be iOS6 version information provided from the sources. If this happens then Podcasts they will have its own related softwares like iBooks did before. which will take Podcasts out of the iTunes and music apps.
There is a gossip that iTunes you will also be receiving broken out of iTunes and into its own application, but there has been no verification on that.