It might be a good idea for the documentation to reflect the tradeoffs more clearly.
Here's a proposed addition to the Secondary Index FAQ at http://wiki.apache.org/cassandra/SecondaryIndexes
Q: How does choice of Consistency Level affect cluster availability when using secondary indexes?
A: Because secondary indexes are distributed, you must have CL level nodes available for all token ranges in the cluster in order to complete a query. For example, with RF = 3, when two out of three consecutive nodes in the ring are unavailable, all secondary index queries at CL = QUORUM will fail, however secondary index queries at CL = ONE will succeed. This is true regardless of cluster size.