It never ever bothered me that you can’t see Gordon’s body, and that his hands don’t touch buttons and ladders… Sure, it’s unrealistic, but it’s not something that’s annoying or even noticeable, unless you specifically pay attention to it.
I think that the act of Gordon pressing a button is equivalent to you pressing E on your keyboard, which satisfies your expectation of seeing a finger press a button, for example.
Maybe in a game engine in 5 years we’ll see something much more realistic, but for now I’m sure this is nothing to waste coding time on.
Mirror’s edge is a good example, but then Mirror’s Edge is more realistic in terms of the human character you control. It’s more about you being skilled with your body, while Half-Life is you being skilled at thinking and aiming, which are more external to the body.