This can't be enabled on databases with existing tables, so for existing users we can either a) add a FAQ with instructions to recreate and let the advanced users do it and let everyone else have larger tables or b) add a migration step to dump to a new file and then replace the old with the new, which may be a risky and not all that easy proposition (given the lack of .dump) but might work...
The steps, by the way, with Firefox closed:
$ sqlite3 zotero.sqlite
sqlite> .out dump.sql
sqlite> .quit
$ sqlite3 db.sqlite
sqlite> PRAGMA auto_vacuum = 1;
sqlite> .read dump.sql
sqlite> .quit
$ mv db.sqlite zotero.sqlite
c0eb1746db