I removed an index from our clustered environment by changing the indexes.conf on the cluster master and pushing the package. However, the data itself is still on disk. Can I safely delete this manually at this point?
As this is a clustered environment you're going to need to remove that index on each one of your indexers if you want it to be completely gone. You can put your cluster in maintenance mode and then stop each indexer issue the following command on each one:
./splunk clean eventdata <index_name>
If you don't do this on every indexer while in maintenance mode the data will continue to replicate and you'll be playing whack-a-mole.