Thanks for sharing your experiences here. I'm sorry you feel you paid too much for the tickets. Although we're not Rail Europe I will try to provide some meaningful feedback:
If I understand you correctly you paid INR 12960 but as the tickets show only € 49 per ticket (so € 147 = about INR 11000 in total) you feel you have paid too much.
You also mentioned prices in US$ you found on the raileurope.com website. Please note that this is a website selling to people in North America. Most of what they offer can only be sold to people in North America (a few exceptions apply). Even though both raileurope.com and raileurope.co.in are Rail Europe sites, they are separate sites and organisations. They're less related than they seem to be, and each has its own prices, promotions and conditions. Furthermore, there are other websites selling the same tickets. You don't have to buy from Rail Europe India. The page myswissalps.com/ traintickets/france/ price lists various options for the country you're currently in (in your case India). So you can buy from any of the others too, like captaintrain.com for example.
I do agree it's a bit weird that tickets show a different price than the amount you actually paid. I think that's because Rail Europe is a sales organisation and does not operate trains. They just sell tickets, like many of the other websites. The original tickets, in this case, are priced in €, so that might explain this. Local websites like the Rail Europe India site offer payment in the local currency, and often a local help desk as well, so that's why you may pay a different price. They take the exchange rate risk away from the customer and booking fees might be a way to cover that.
I assume the shopping cart showed the exact amount you were about to pay. If not, that's definitely not good. If it did, I don't think they're cheating. It's a matter of a complicated market with lots of options to choose from as a traveler. Many other Rail Europe websites (for Australia, Hong Kong, etc.) work in a similar way. This is not about Indian consumers. As a matter of fact, many of their websites, including the Indian one, often offer very low prices as well. Last year for example, Swiss rail passes for Indian customers were very cheap. Travelers from Europe could not buy a pass for those low prices, but it wasn't a matter of cheating European customers. Rail Europe happened to fix their prices before the €/CHF exchange rate went down. It was just a twitch in the market causing this.
I am not sure what Rail Europe means when they replied "when you made the booking the discount was not available, hence you did not receive it". Ticket prices for high speed trains like the one you booked change by the booking date, travel time & date and by promotions offered by ticket resellers or train operators. It may very well be possible that prices dropped between the moment you booked and the moment they actually issued your tickets. The reverse could have happened as well, and they would not have charged you extra in such a case. I think this is what happened, but please ask Rail Europe if you'd like to verify.
Again, we're not Rail Europe. I do know a bit more about the market than the average traveler. I can definitely confirm that this market is complex, which can easily result in a bad experience. Nevertheless, I hope the above was helpful. And I hope you'll have a very pleasant trip!