Not saying SQLite wasn't the issue here (impossible to tell based on the information provided), but I've seen a lot of webapps with highly inefficient queries because developers either didn't understand what the ORM was doing or didn't bother to optimize. In a Django app, prefetch_related can make a huge difference (or joinedload when using SQLAlchemy or better initial filtering when using raw SQL).
We used mostly raw SQL. Django ORM is good for CRUD app, but anything analytic style app, it's more painful than it should be. I'm not blaming Django, just we picked the framework for CRUD work and had to retrofitted to do analytic because of requirements.
