First think I would like to say is: the writer is biased because he is from BARC. Any BARC scientist has a solemn pledge to oppose the deal, because it is definitely not as per their wish. I am not criticizing Mr Prasad, but I am just saying he has a personal interest in it.
Second, the apprehensions raised by him is unfounded. The involvement of foreign companies and fund will only help to improve the potentiality of the nuclear sector. The writer is concerned about future fallout if supply stops in case of India takes any adverse decisions. But before we jump into that discussion, we need to learn what do we mean by adverse decisions? In what context that situation may arise? I can only think about one a possible situation where India tests an atomic bomb and consequently the supply stops. But that has been debated endlessly since the beginning and it has been concluded that the safeguard agreement does not have any clause to prevent India doing so and more importantly, even the supply is cut off, India can take "corrective measures" to tackle the situation.
Any way, I think BARC scientists will always have a one sided view on this and we should not give too much importance on them.