You can use several other 2FA apps such as Google Authenticator if you do not trust the Microsoft one, they are compatible.
That said, personally I do like the Microsoft Authenticator app very much, it's just a single tap on the phone to confirm the 2FA login, which is much more convenient than retyping a code. Disadvantage is that the Android version of the Microsoft Authenticator app can only have one account, I could not connect a second 2FA service (LastPass) to it.
MS 2FA fails, you can still use IMAP to fetch email and stuff, without 2FA. So it's only partial implementation. Of course it prevents "completely taking over the account", but even if it's enabled you can still do a lot without providing 2FA code.
That said, personally I do like the Microsoft Authenticator app very much, it's just a single tap on the phone to confirm the 2FA login, which is much more convenient than retyping a code. Disadvantage is that the Android version of the Microsoft Authenticator app can only have one account, I could not connect a second 2FA service (LastPass) to it.