PIM-2833: Use manager to delete entities

| Q                    | A
| -------------------- | ---
| Bug fix?             | N
| New feature?         | N
| BC breaks?           | Y
| CI currently passes? | ?
| Tests pass?          | ?
| Scenarios pass?      | ORM: 1023 - ODM: 66
| Checkstyle issues?   | N
| Changelog updated?   | TODO
| Fixed tickets        | PIM-2833
| Doc PR               |