Using force.com migration tool with ANT allows you to deploy destructivechanges.xml. http://www.salesforce.com/us/developer/docs/daas/index.htm
The sample package provided includes a destructive changes example.
Advantages of using this over doing it straight from Eclipse are:
- You can replicate the operation against different sandboxes / production by running the script again. So for example you can first test that the destructive deploy works as you want in a UAT environment and then run the script connecting to production.
- You don't tie up your eclipse waiting for a response (for a big org a production deploy takes significant time)