As a database person, this was hard to read. I wanted to find out what the problems are and solve them.
A db table with only 10k rows? Even a full table scan should be extremely fast.
And with SQLite - which I assumed runs in-process, but even if not, surely is running on the same physical server? Faster still.
Of course, the magic phrase in my head is “create index”.
I hope Julia posts an update!
Edit: I highly suspect the “slow deletes” problem is a classic “n+1” problem suffered by many ORM users, until they come to understand more about the underlying db interactions.