If a script passed to run_script() (or a straight SQL string is passed to run()) has bad SQL in it (in my case, it was attempting to create an index that already existed), the method will fail with

** (geary:744): CRITICAL **: sqlheavy-database.vala:167: Unable to execute queued query: The database file is locked

After debugging, it appears the problem is that run_internal() is throwing an exception causing the Transaction object to be dereferenced, and the ROLLBACK TRANSACTION TO SAVEPOINT command is failing with Sqlite.BUSY.