Just use a big gun when you get to the hideout (I prefer the Magnum and its subsequent upgrades). It worked well in clearing out the other guys. Then, use hand-to-hand to beat the furnace dude up within an inch of his life...it makes him easily moveable and you toss him in without too much issue.
Thats the only way to whack him, if you shoot him, you have failed the mission, as the only way to whack him is by throwing him in the furnance....
