You may be the only one. Frankly, that would send Gordon careening over the Moral Event Horizon. He's a jerkass protagonist, yeah, but he's not a total psychopath. He doesn't kill people for fun, not even the soldiers. He's gone out of his way to avoid soldiers before, and has mentioned that killing them is one of those things that he'd put off if he had any other option.
And it would make him unlikable for a lot of people. Or it would for me, at least. At the moment, Gordon just wants to survive. He's more than a bit crazy, and he's not a "hero" in any sense of the word beyond the fact that he's the protagonist, but he's not deliberately going out to kill people, either.
Let's put it this way: The military is actively trying to kill him, but the scientists and security guards are just innocent bystanders. Shooting the soldiers who are already shooting at him, or who are obviously plotting to kill him the second he shows his face, is self-defence. Slaughtering the scientists and security guards who mean him no harm, and who want to help him (regardless of how crappy they are at it), would be flat-out murder.
I get that he's threatened people before, but he's never gone through with it, and he's usually gone through hell right before his freak-outs. I'd be more than a bit pissed off, too, and probably willing to yell at people, threaten them and wave a gun at them -- especially if they were the reason I'd just gone through an extra obstacle course of death. I mean, if I'm getting assaulted by aliens who zap me, shoot me with bile, and try to attach themselves to my face, and suddenly the military shows up and also starts trying to kill me, I wouldn't be at my most rational or patient either.
Gordon just wants to get the hell out of Black Mesa and go home. Or to India. Whichever. He doesn't seem particularly interested in or approving of the wholesale slaughter of unarmed civilians.