Gordon Freeman

So how does a theoretical physicist automatically become a killing machine? Do both killing and this hard science work the same Brain region?

No, he was wearing a powerful suit that allowed people into xen. Also he was very very lucky.

He's seen Die Hard like.... Six times

Even Breen questions why the fuck Gordon's still alive and why cybernetically-enhanced armies can't put him down for good in HL2. Gordon's got literal plot armor, and he's damn lucky; he's got something watching out for him in almost every situation, to some degree or another. Unless you fuck up with something like destroying a vehicle you need or killing an important NPC, then Gman drops you like an ugly baby.

plus he's had weapons training

The suit was extremely powerful designed for fighting aliens and exploring hostile environments, he also had a god like being watching over him.

hes got the HIV suit and an inter-dimensional being (gman) helping him

Suddenly, I'm a lot more optimistic about my own odds surviving an alien invasion.

Gordon freeMAN

I'm pretty sure G-man doesn't care if you bite a bullet, considering you can Game Over just fine. Unless G-man's canon powers are the save and load menus.