Just before the massed Alien attack on the operations center even Hicks had come around to the idea that Burke had to be killed.
RIPLEY: You know, Burke, I don't know which species is worse. You don't see them fucking each other over for a goddamn percentage.
HICKS: All right, we waste him. No offense.
And then the Aliens cut the power. Ripley still wanted him alive, but Burke had to believe his chances of survival were poor remaining with the marines, who all wanted his blood. So the first chance Burke got he put distance between himself and the marines, hoping that the Aliens would take care of the marines for him. That would leave only Bishop, who presumably would submit to Burke's authority. At that point Burke might be able to salvage something of his personal mission. With Alien DNA splashed liberally around the compound (the things drip slime everywhere) Burke might be about to scrounge a sample, but at worst he'd save his own crafty skin.