We've been using MSSQL with moodle since 2011. We've gone back and forth a bit between the freetds and MS sqlsrv drivers.
With 3.1 and previous there's an issue with large backups related to session tables for sqlsrv which I think gets resolved in 3.3. We'll be using sqlsrv with PHP 7 when we upgrade to 3.5 later this year.
Using MSSQL used to be a problem with earlier versions of moodle -- especially 3rd party plugins, which often used db-specific sql; but in recent years we haven't had any real issues.
We use MSSQL because it's the supported platform at our college, and it allows us to focus on moodle admin and not have to do db admin as well. As a benefit we can do cross-db queries for integration and reporting relatively easily.