Some advice needed here on software applications which can access my hotmail email.

I have installed on my work PC the outlook hotmail connector which allows me access to my personal hotmail. Subsequently I turned on 2 factor authentication for my hotmail, meaning I use the Authenticator app to type in a code after supplying my normal hotmail username and password.

Outlook, on the other hand, is still syncing with my hotmail account and collecting emails - meaning that the additional security is not being applied here.

This seems like an enormous security hole - If someone got hold of my hotmail account credentials and password, they could presumably use this menthod to get access to my email, and avoid 2 factor authentication altogether.

Can someone please clarify how I can make my applications (like outlook) secure with 2 factor authentication enabled.