Rao's reply in Computational Linguistics: http://www.cs.washington.edu/homes/rao/IndusCompLing.pdf
Also other articles at: http://www.cs.washington.edu/homes/rao/IndusResponse.html
Edit 1.
An aside:
Being a logic student who uses probabilistic machine learning, Farmer's use of the words refutation, proof etc. make me despair. This web page is an example:
http://www.safarmer.com/indus/simpleproof.html
Rao is much more careful and nuanced in his methods. Using time-tested logic and math. http://www.cs.washington.edu/homes/rao/ScienceIndus.pdf
" As clearly stated in the last sentence of the paper, our results provide evidence which, given the rich syntactic structure in the script (and other evidence as listed below), increases the probability that the script represents language."