Blown headgasket

My 2001 pontiac grand am gt, 6cyl, 114,000 miles started showing low coolant a little while ago. After adding numerous times it finally started getting really hot one day. I took it to the dealer who said it was a leak in the intake manifold which cost me $800 to repair. Two days later it started doing the same thing, getting hot, so again I towed it to the dealer and now they are saying I blew a headgasket and say that something that would normally cost $1300-$1500, they're only going to charge me $1000. They said they didn't even check anything else because they figured it was the leak that was causing the problem. Does this sound right? Should I have to pay the $1000 or just $700 since I've already put $800 into the car. Would the leak have even been the problem in the first place?