This problem has been resolved to some extent. Cointracking.info is now taking INR/BTC price from bitcoinaverage.com. However, bitcoinaverage.com averages prices from BTCxIndia, Coinsecure and Localbitcoins. Zebpay and Unocoin apparently are not factored into the average price, which is unfortunate because most people in my opinion buy BTC from Zebpay and Unocoin.

In any case, it's still better than converting USD/BTC prices to INR/BTC.