To be fair Mr. 47 really isn't a bad guy. Sure he kills people for a living, but this is what he was genetically engineered to do. Shoot, the beginning of the second game he'd all up and retired and was chilling at a church in Italy where he had befriended a the priest who was in charge and he was trying to atone for his past 'sins'. That all went to hell when the priest was kidnapped by his enemies, and he had to get back into the business just to save his friend and spiritual advisor's life.
Mr. 47 generally only takes out really bad dudes. Drug lords, pedophiles, dictators, war criminals. The people who everyone knows are bad, but they can't be dealt with legally.
And this should really amuse you Eldar, in #2 there's evidence of 47 converting to Catholicism. :D