After watching the Season 2 DVD special features it's pretty crystal clear that Kellerman isn't dead. I think that Kellerman was the guy that Whistler took out on the boat for "measurements." It's clear from Season 2 that his loyalty is shakable, which makes me think he is a double agent or something and makes his "confession" at the end of Season 2 all the more interesting, maybe he felt that this would smoke out the guys that screwed him over? And maybe he was taken out of the president's circle because they were suspicious he was a double agent?
So they stage his death, but the interrogation doesn't go well, since it's Kellerman.
Hence the Panama plan, a shift in strategy. If you can't get the agent to confess where he went, and more importantly who he talked to, you get the guy who provided the ride to do the best he can. The real question is, what would Kellerman have been doing out in the Pacific? Selling intel?
Not too much of a long shot, and I think one of the more realistic plot arcs -- time machine, and Whistler's the engineer?
And if all this isn't true, I hope he's still alive and helps break the boys out of Sona the ole' fashioned way, with guns and manliness.