checkpoint docs are not deleted after replication spec is deleted

When replication spec is deleted, running replication instance needs to be stopped, and checkpoint docs need to be deleted. We used to handle this by

1. deleting checkpoint docs
2. stopping running replication

This is not 100% reliable since checkpoint docs may get recreated by running replication at step 1 due to periodical checkpointing. The matter is made worse by  recent changes where replication would always create a checkpoint before stopping. As a result, checkpoint docs always get recreated in the stop sequence.