As the component was already deleted from Content Manager, you can capture the transport package and manually edit it to refer to the component you wish to delete. Then place it back in the deployer's incoming folder for the deployer to process. This way the deployer is responsible for removing the records and preserving database integrity.
1. In the deployer's cd_deployer_conf.xml, set Cleanup="false" in the Location element. E.g.
<Location Path="c:\tridion\incoming" WindowSize="20" Workers="10" Cleanup="false" Interval="2s"/>
2. Take another component present in the same publication and unpublish it.
3. Navigate to the deployer's incoming folder and copy the generated package to another location.
4. Unzip that package and open the instructions.xml and the transaction.xml files.
5. Change the tcm id present to match the id of the component you want to delete.
6. After confirming that you only have references to the id of the component you want to delete, zip the package again.
7. Place the package in the deployer's incoming folder. The deployer will process the package and the component will be unpublished.