VR didn't want to kill them, he only wanted the proof, hence the reason he kidnapped Prabha, was for Mahesh to come and save her by giving him the proof. As you said, Mahesh could've made a copy, one for himself and one for VR, so even if he give VR the memory card and VR destroyed it at least Mahesh would've had his copy to prove his innocence. I don't have a problem with Prabha's last line, VR was aiming to shoot Mahesh, not Prabha but she came in front him and got the bullet instead. Even if they wanted to create a death scene, then they could've soon Mahesh getting killed and Prabha being alive. Prabha being there wouldn't have taken away the main plot of the story which is the bond between Darpan and Ganesh. They could've soon her going into a coma or something when she got shot.