No I don't think they will be sympathetic at all. Faith seems like the closest one to that but I'm sure she is just as crazy. John and Jacob just seem utterly insane and enjoy violence and Joseph from everything that has been shown of him, really doesn't care about taking peoples lives..
Granted I'm most excited for this game because of them all and I'm sure I will really love their characters but I don't think I will feel sympathy towards them, but far cry writers could throw in a twist plot and well I just cant say for sure till I play the game