Will's been one of my favorite character's I think. Just think about being in his shoes, doing your job on reporting leads you to be captured by your best friend's dad, then beaten up, then rescued, then suddenly you are a drug addict and then you work for the CIA. Kinda cool..the tough way to start working for the government but I hear they have good benefits.
Of course Jennifer Garner on the show is obviously a favorite...for reasons that will be known only to me (and the rest of the male population).
If they are going to kill off a main character there are bunch that they could without ruining the show, Francie of course will get hers soon enough, but her, Dixon (sloan's going after him soon isn't he?), even Sydney's Dad could be a target. I think this show could work with pretty much everyone replaced except Jennifer Garner. Her character would just need to evolve to keep up.