Having studied these books a few hundred times, I have come to a conclusion about what the Chtorran infestation really is.
I think that the Chtorran invasion is a pan-spermia phenomena with shambler trees as the prime source of the invasion. In The Season For Slaughter, McCarthy and company investigate a stable shambler mound in Mexico. Within the mound they discover what appears to be a biological factory producing components of the Chtorran ecology, from millipedes to full-on Chtorr worms. One toss away comment by McCarthy was that shambler tree seeds have withstood testing by dropping from orbit.
Hypothetical planet Chtorr, supposedly at least a half billion years further along the evolutionary chain, and within a suspected 30 light years of Earth, is spewing shambler tree seeds in all directions. Some fell to Earth and started the cycle, but I don't think there's any reason not to suspect that even the planet Chtorr might not have been an invader ecology. Perhaps the Chtorran infestation has been spreading throughout the Orion arm and it's just now reached Sol? The prisoner/rescuee picked up towards the end of TSFS exhibits some of the ways that the Earthian ecology will be adapted to Chtorran ecology - which goes back to the pan-spermia idea. Perhaps the shambler trees were first, but as they proceed through different ecologies, they pick up different biological samples and incorporate them into a synergistic whole.
Regardless, whether or not there's an intelligent species directing the infestation is irrelevent. I think what the Chtorr ecology demonstrates is that intelligence is not the final word in evolutionary survival. Several species of Chtorrans have exhibited various degrees of intelligence and ability to communicate, yet remain in some ways dictated by their instincts and position within the Chtorran ecology. Bunnydogs, bunnymen, meeps, and worms have demonstrated the ability to conceptualize, plan, react to stimuli, and communicate. However, intelligence for intelligence's sake seems to be missing and, perhaps, is really an evolutionary dead end.
I suspect the only solution that really is viable is sterilization of the planet and repopulation from the gene banks and reserved populations on the Moon and L4/L5. I truely hope he doesn't resolve the issue by 'remodulating the beeping machine on deck nine to save the day by the end of the episode.' Be kind of an interesting ending if the human race is driven off world completely and Earth becomes an alien planet. Depressing, but would be different.