Clean up repositories with symbols correctly

Summary: We currently try to delete symbols by ID, but the table has a multipart primary key and no `id` column.

Test Plan: Ran query locally; had @JThramer verify fix in his environment.

Reviewers: btrahan

Reviewed By: btrahan

CC: JThramer, aran

Differential Revision: https://secure.phabricator.com/D4626