Depending on what you need to do with Mongo analytics, it might be worth some time to look at other analytics platforms that do natively support MongoDB. There are a few popping up, like Knowi and Slamdata. They eliminate the need to move your MongoDB data to a SQL store and the bottleneck that creates. I know that Knowi supports MongoDB Atlas (cloud), not sure about Slamdata.
It would be nice to avoid using the BI Connector in Looker but not sure how you can right now. I just wanted you to know there are alternatives out there in case that was a viable option for your project.