Currently, all custom repository methods boil down to those found in 
SimpleCassandraRepository, which delegate to a 
CassandraOperations instance.  I looked, and the repository methods (
CassandraQueryMethod) don't yet support accepting a per-method 
QueryOptions or 
WriteOptions argument, nor does the 
@Query annotation, although the underlying 
CqlOperations methods do.  There is also no way to define per-repository-type or per-repository-instance default consistency levels, or per-template-type or per-template-instance default consistency levels, so this looks like an enhancement request.
Sorry for the delay in responding.