The Sub thing is not just like Kulbhashan which was caught red handed though whatever you exemplified is never seen in Military that too between arch rivals like Pakistan-India. We know, many of times A/Cs are being radar locked to tell that "Stay Away". Rules of Engagement (RoE) must kept in view during operations and we are not some kind of back stabbers like the enemy (there is an example but no need to drag in merely not to diver the topic).
The Surrendered must not be shot at all, only cowards does that. We detected them, they acknowledged and surfaced, turned back (a white flag to say) and the message sent while on other hand PN happy with its such operation as well as the Nation that surely, security is in competent hands. I would rather say, it was more practical and better than such type of engagements during exercises to learn, which proved preparedness of PN in these conditions on real time bases specifically with respect to the Subject alone.