You will always see a button to access messages from your Team App. However, if you click at the bottom of the App, go to Settings> Messages, you can choose not to load messages upon log in.
If you close the messages window, it should not open the next time you launch the app, but you will still see notifications. In the near future we will be releasing a setting option that will allow you to disable messages completely.
You can remove the Messages feature from the Team app by clicking on your name on the app's window > going to Settings > Advanced and making the appropriate selection.