http://www.sciencemag.org/content/324/5931/1165
You also mentioned the Brahmi script is "unquestionably based on the scripts of the ancient Near East". That is also news to me. Could you provide citations, please?
The real controversial implication, IMHO, of studying ancient Indian languages is that Sanskrit (used over thousands of years and refined by rigid grammar rules by e.g. Panini 500 B.C.) may actually be the language from which Latin, and hence many European Romantic languages, developed.
http://mutiny.wordpress.com/2007/02/09/sanskrit-mother-of-eu...
That's probably worth diving into, if you are genuinely curious. As the Welsh linguist Sir William Jones said,
"The Sanskrit language, whatever be its antiquity, is of a wonderful structure; more perfect than the Greek, more copious than the Latin, and more exquisitely refined than either, yet bearing to both of them a stronger affinity, both in the roots of verbs and in the forms of grammar, than could possibly have been produced by accident; so strong, indeed, that no philologer could examine them all three, without believing them to have sprung from some common source, which, perhaps, no longer exists."
[edit- link added and fluff redacted. :)]