What's the best way to completely clean an index in a clustered environment?
Currently, there is not really a good way to do this as cleaning the event data from an index will just get replicated back from another cluster node.
That being said, there are two not quite so nice ways of doing it.
For the 1st option, you may find the following link useful:
http://docs.splunk.com/Documentation/Splunk/5.0.3/Indexer/RemovedatafromSplunk#How_to_delete
For the 2nd options, take a look at the documentation here:
http://docs.splunk.com/Documentation/Splunk/5.0.3/Indexer/Setaretirementandarchivingpolicy