Now JJ loves his incesteous subtext (just thinking of Sloane's mixed paternal and not so paternal feelings for Sydney) occasionally, but I very much doubt it in this case.

I used to fervently wish Vaughn would get killed off for three seasons, especially in season 3, but in 4 he actually had some interesting moments. Though if a regular gets killed off, he's still my first choice, so my prejudiced guess is that the cliffhanger is a way for prepare for Vartan to leave the show.