Your bolt probably rusted to the metal sleeve inside the stock trackbar bushing. Mine did, it was a real pain to get out. If you are going to throw away your stock trackbar, you can do what I did and use a cut-off wheel to cut the trackbar off the bushing, then cut the bushing down to the sleeve. I was able to put a pair of vise grips on the sleeve and after heating it up with a propane torch it popped free pretty easily.
Did you get the nut all the way off? The track bar bolt goes into a nut with a "flag" on it - you should be able to see the flag sticking out the bottom of the trackbar mount.