Cassandra - WHERE clause with non primary key disadvantages

From within Cassandra itself you are limited to the options that you have specified above. If you want to know why take a look here:

A Deep Look to the CQL Where Clause

However if you are trying to run analytics on information stored within Cassandra then have you looked at using Spark. Spark is built for large scale data processing on distributed systems. In fact if you are looking at using Datastax (see here) which has some nice integration features between Spark and Cassandra specifically for loading and saving data. It has both a free (Community) and paid (Enterprise) editions.

Please, try to use IF in your query:

UPDATE [keyspace_name.] table_name
[USING TTL time_value | USING TIMESTAMP timestamp_value]
SET assignment [, assignment] . . . 
WHERE row_specification
[IF EXISTS | IF condition [AND condition] . . .] ;

see https://docs.datastax.com/en/archived/cql/3.3/cql/cql_reference/cqlUpdate.html