Why not. Even if you get 100 drones intruding from Chinese side, with each Rafale carrying over a dozen BVR for a dedicated A2A mission to bring down those many Drones. If I am not mistaken, even the MKIs can track over 10 targets at a time and hence they can also do a dedicated A2A mission to bring down those many drones.
I do not think there is any scenario that the Indian forces have not gamed.
There are two flaws with that theory -
a) Cost - The drones which will be coming in are super cheap (talking about the quad copter style ones - which few days back the Chinese were using for food delivery), and our BVR missiles are super expensive and apart from Astra, all imported. How do you see this panning out, if we use our BVR AAMs to take out their cheap drones?
b) Numbers - Again, if we exhaust our AAMs to take out their drones, how do we replenish during the conflict? How many can we get and how fast?
Remember, it is not just the drones, they have an airforce of conventional jets as well. With the above strategy, we won't have any missiles left soon enough to take out their main stay jets/bombers.