Below, you're looping through the result set twice, to transform the key and value individually, when you can actually do both in a single trip:

    for(Entry<Long, Set<TObject> entry : chronologize){
        result.put(Timestamp.fromMicros(entry.getKey(), Transformers.transformSet(entry.getValue(), 
            new Function<TObject, Object>() {
                
                @Override
                public Object apply(TObject input) {
                     return Convert.thriftToJava(input);
                 }
            }       
    }