In the new Android 5.0 update, GMail was made to be available as the only e-mail app you would need. Instead of having to have 2 different email apps for gmail and exchange, it would do everything for you. Now remember, your exchange email is completely separate from your gmail, so there is nothing happening to your e-mail, it's not being hijacked by Google or anything, the app is just a place where it is getting delivered. If you still don't want them in the same app, then you can always install a different email app to handle your exchange e-mail.
Download an e-mail app, such as Nine that will handle your exchange e-mail in a separate app. First you are going to have to delete the exchange e-mail from your GMail app, then install the new email application, then add it to the new application.