The only way to prevent this is to remove elevated access from the player's computer. This has been done with varying levels of success on consoles, but even then it's only a matter of time.
But I also think a lot of the hackers in both GTA and CS are cheating in ways that no regular user input could trigger, they're compromising the software at a lower level than that.
The bigger problem is that even with input recognition, one of the biggest problems are wallhacks, meaning you can see other players through walls which is an advantage that's almost as large as aimbotting in tactical shooters like CS.
