You do not have to deactivate a Contact Tracing Application. The misunderstanding is probably a result of some shrill forum members trying to stir up fear.
Even if the API is installed, you still have to install an app separately for anything to happen.
Furthermore, /e/ has a nice specialty in store for the paranoid: even the Contact Tracing feature of microG has to be installed separately in the future.
For details see this interview: https://community.e.foundation/t/microg-what-you-need-to-know-a-conversation-with-its-developer-marvin-wissfeld/