In all likeliness, the reason Gman chuckled, is probably due to him thinking about how he knows Eli is going to die anyway which would defeat the point of the warning until you realize it could just very well be a warning to the player disguised as such. If you listen closely to the scene you’ll notice he chuckled after mentioning Black Mesa & we all know how that ended up. He also laughed after mentioning the vorts being your friends, so make of that what you will.
Eli being able to resist the Advisors, while both being pretty amazing & unexplained, making him an alien would seem pretty random at this point (now that he’s dead) because if they were going to work that into the plot, revealing such while he was alive would have been made far more interesting if he were alive to converse with the other characters about it.
It seems like MarshmallowRadiation had the best explanation so far. It makes sense for the advisors to want to get to his brain as fast as possible & without the risk of damaging it by throwing him & probably didn’t expect him to fight back so readily on account of the ambush. But I still wonder why the first one there wasn’t also the one to suck his brain.