Eli Vance isn't dead. He's in collusion with the Brain Sucker bug-I mean the whatchamawhosits (sorry, I was in Starship Troopers mode for a second), to take out the G-Man, a mutual enemy. You see, in spite of their incredible power, the Advisor's NEED Eli Vance alive to bait Freeman, and by extension, the G-Man, and bring the battle to their place of choosing.
Where is that? You might ask. Why, isn't it obvious? The Dark Matter explosion thingy is REALLY a portal to another world (not Xen), in fact, the home planet of the Advisors, where a Council is waiting to judge and summarily execute the G-Man, who's subversive tactics to twist those who would hire his pawns into continuing his genocidal war with the Advisors has lead to millions of dead.
The combine are really a reactionary force that's fighting the G-Man's pawns and trying to get him into a position to break his power.