You can use the Graph API to send emails from your service account. Where you are going to have a problem is with identifying logged in users. An AAD token will be valid for your site even if the user originally signed in somewhere else, so logging signins isn't foolproof. Unless your users specifically sign out, the token will also be valid past when they stop using the site.
If you wanted to go down this road, then doing some logging of user actions and then sending the email to users that have been active within X amount of time might be an option.
If your goal is to notify users and you don't need an email specifically, then you might want to looking into using websockets or something similar to send notifications to the users within their browser.