What defines "good"?
If Not God? If Humanity is this bad WITH religion imagine how bad would they be without it?
You could even begin by meeting him on his own ground...(in fact I think you should ALWAYS do this.. quoting scripture is not convincing to anyone without faith in it..and God is truth, and he is found there Always, no matter how the truth is arrived at or expressed. Scripture is NOT PROOF to anyone who doesn't believe, and you will loose ground and credibility if you attempt to use it in this debate (as proof - as illustration its fine..) )
SO Accept for a moment his premise that there is no God and Religion is just a Tool used by mankind. Like any tool, it can be used for Good or for Evil, could it not? But if there is NO FORCE in the universe defining Good or Defining Evil, and such determination must be left to the individual , he must admit that there are no absolutes.
By teaching of a higher power- of a God with rules, of definitions of right and wrong, and having a society all following those rules you avoid the moral-relativism-free-for-all and have a means to regulate and encourage "moral behavior" (however defined) and thus benefit all people living within that system by having a common set of rules that DO NOT rely on a the barrel of a gun to be enforced, but are obeyed because of a personal and deeply held belief in religious doctrine.
Is that not for the "greater good"? The wars that religions have been involved in, encouraged, or have been the cause of, are simply the Macro version of the conflict that would occur between each and every human being if there were no religions to define and support a moral code within a society. Given that religions reduce interpersonal conflict and violence within a society that (largely) adheres to them, and that wars caused by religion usually have as their aim, the imposition of that same moral system on a greater number of people which would then further reduce violence and interpersonal conflict in the long run, would not the "greater good" dictate that a single system imposed by force be better for everyone? Would not a world entirely peopled with Jews, with Hindus, with Muslims, or with Christians be inherently more peaceful than a world of Atheist individuals all of whom believed themselves capable of laying down their own (and conflicting) moral laws? No human society can long endure without a shared moral system. Our country is proof of it as the conflict between liberals and conservatives - both with very different ideas of right and wrong, demonstrates.
At some point he will likely retreat to Spock's "The needs of the many outweigh the needs of a few" and as soon as he admits the principle of "Gemeinnutz geht vor Eigennutz" ("The community comes before the individual") you remind him that philosophy was written around every Nazi coin and that Hitler firmly believed killing all of the Jews was for the "greater good." and ask him to tell you by what principle or rule we can distinguish what he sees as "good" from what Hitler saw as "good" - there being no God, who can see all ends, to help sort that out.
I think you could easily trap him in an " Ends Justify the means" statement where someone is harmed...
Is it right to deprive people of weapons (guns) with which to protect themselves if on net it saves lives even if some people are harmed? Is it right to allow abortions as a separate and unique human being is killed? Is it right to force people to contribute or support causes which they find ( in contradiction to a majority) immoral or reprehensible (like abortion)?
Force him to admit that he feels a "majority opinion" is the definition of "right" or "good"
You can then remind him that the Majority once felt enslaving Blacks to be "good" - not only for the society but for the blacks themselves.
From there I don't see where he could retreat to. Maybe some statement about not doing "harm" to others, but having already admitted to a philosophy where the "ends justify the means" - that harming some for the good of whole is justified, you go for the kill , point out the circular reasoning and force him to admit that the principle difference between his ideas and those of Hitler is simply the difference between of his OWN selfish desires, and his own selfish opinions, his own values, and those of Hitler -- neither of which are universal, and can only be imposed upon others at the point of a gun.
You can therefore then return to the original question - "Does religion help more than it hurts?"
Obviously Religion benefits mankind EVEN IF we accept his premise that religions are entirely fictitious stories used to justify the impositions of such moral systems - because the reduce intra-personal conflcit within a society without requiring the use of force of arms. When force of arms is used, its an abuse of the tool to be sure, but by his own JUDGEMENT, in which the ends justify the means, he cannot condemn the use of the tool in such a way, since his views of right and wrong are no more valid (or invalid) than those of the next person. If there is no God, then Might makes Right, and let the most powerful Religion win.