No one could tell you this for sure. In India lots of crazy things might happen. You shouldn't be surprised if such a move is going to be forced upon the IITs by the GOVT of India.
The chances are very less for IITs to come under the purview of this system. IITs conduct the most tough exam in INDIA known as the IIT JEE, and it wouldn't make sense to scrap that exam and dilute the quality by conducting a common entrance exam for all Engineering Entrances.
So the chances of IIT JEE being conducted are high, and no it shouldn't be history anytime soon.
All the Best,
Ashwin (IIT Madras).