I don't want to get to get into a theological argument, but just a quick answer to the last part of your message.
That's more or less Pascal's Wager, mixed with some "Is God good if he lets innocent people suffer?".
There was a philosopher we studied (sadly I forgot his name) that made the case that despise there are children being crippled and dying, among others, God was still good. His argument was that God wasn't interfering not because he will evil or impotent, but because of free will. Actively interfering would interfere with the free will he had given to mankind.
I do think this is an incorrect argument (why does something like polio exists, and if it exists for a purpose why are we allowed to eradicate it through vaccines?), but for the sake of it, let's just go along with it.
If God does not want to interfere because of free will, he will not in this case.
If God is impotent, then even if he wanted to do something he could not.
If God is evil, or at least does not care about humanity, he has no reason to act.
We have no reliable proof that God ever acted to prevent evil, there's little reason reason to believe he will start all of a sudden. So praying to God, even if it exists isn't going to change anything.
If by God's mercy you meant salvation after death, like going to Paradise or whatever, it gets a bit complicated. Those people that were killed were drinking, listing to music and probably doing a lot of things forbidden by the bible in the first place. Is being savagely killed by fanatics a good enough reason to be given mercy? And are prayers going to change anything, like God saying "I was going to send him to hell, but John prayed for him so I'm gonna change my mind."? That does not really go with the belief that God is omniscient.
To sum it up, praying seems pretty useless to me. It can help people deal with the situation at a personal level, but it's not going to help the dead.
On the other hand, praying goes in hand with faith, and putting faith above everything. The same faith, no matter in what it is, or how misguided it is, that convinced the guys to go and blow themselves up.
Maybe if we had less faith in the world, and more rationality and thinking, this kind of things would not happen. I think that's the message the Parisian wants to convey, let's battle blind faith with something more than more faith.