In the latest release of Microsoft Teams app there is now a setting that allows a user to disable Skype for Business integration for themselves. This is easily done by going to Settings | Notifications | Skype for Business Integration.
This essentially turns off the ability to send and receive Skype for Business instant messages to and from contacts that are not using Teams from inside Teams. (they will need to use Skype for Business for communicating with users only using Skype for Business) It seems the main issue this setting is addressing is the issue that a Microsoft Teams users may receive an incoming Instant Message toast in Teams and Skype for Business apps.
Skype for Business integration is enabled by default, and I suggest before you just disable it, take a moment to make sure you understand the integration more fully. For a more in depth article on how Microsoft Teams and Skype for Business integration read this article.
Enjoy Microsoft Teams! (and Skype for Business!)
To see more Microsoft Teams User Tips:
[Video] Learn Microsoft Teams in 5 Minutes: