I have some ideas, like getting rid of the weapon skills altogether and add some survival based skills focused on guns, like becoming good at making weapons (although repair could be used for such an end, as well). What could be done? I don't know exactly. But should it, in a realistic game setting, be possible? Should someone with a sledgehammer be able to take, heads-on, on someone with a shotgun? Whatever the answer for these questions, the melee and unarmed skills become wasteful spending of skill points. Now, how about melee weapons? It really makes a melee weapon character nigh impossible.
You can work around it by making skill not affect damage, but affect gun wobble and maybe even critical hits. In that setting, spending skill points in Guns for making more damage, for example, becomes pointless. To use your example, one shot to the head = death. Some of them you can work around, some you just will have to ignore. The thing is, Fallout has some RPG aspects that break when you try to implement as much realism as possible. Many games implement RPG aspects nowadays, I like the most realistic ones.
For me there's no balance between realism and the RPG aspect the best RPG, in my opinion, is the one which implements more realism into the game. That said, I currently live in doubt regarding that subject. All the mods I search for are mods that bring more realism to the game, no exception.