Well, if you got the bolts out, don't worry about loosening the nuts until they are flush - the concern was that you not mushroom the threaded part of the bolt when you were pounding them out with a hammer.
What is probably holding them in is the fact that there does not seem to have been any antisieze put on the metal nipple of the bushing when it was orginally installed in the body of the car. Dissimilar metals, water/salt/time, etc. - the two parts essentially fuse together, making it extremely difficult to remove the old bushing in one piece.
This is a comparison of a full bushing, and what was left when mine came out of the car:

The end that is left in the car has to be removed, and it is a bit of a pain.
I just used a long pry bar on the subframe to essentially snap the end of the bushing off, then Dremeled it out. Unfortunately, there is no access from the top to drive it out, unless you can somehow thread a bolt into the bushing material from the bottom and then smack it out with a drift from the top.