I work on a certain other open source LMS that stores some of its data in Mongo but has been gradually moving it all into a relational db.
It is true that the (home-baked) ORM we use on top of Mongo provides an abstraction layer which makes parts of the migration easier, but truly finishing the migration has and will feel like a long, gradual rewrite.
That's because Mongo and its "no-SQL" patterns permeated our original architecture. JSON everywhere, layers of caches to handle the inefficiency of complex Mongo queries, stringly-typed fail-quietly semantics, all that sort of fast-and-loose stuff. Truly moving to relational data (Django models, in our case) means replacing all those old patterns with, you know, thoughtfully designed data models and efficient SQL queries. Otherwise, the LMS would just be a Mongo app awkwardly grafted onto a SQL database.
Yes we'll use an ORM in the future so users can use their preferred database (sqlite for example), SQL Model by tiangolo & SQL Alchemy are great candidates!
It sounds like you're not using an ORM if a rewrite is required?