II've seen this problem many times. The solution is different each time depending on how much the bolt is deformed. There have been many valid answers to your problem, again it will depend on how bad the bolt is deformed/partly sheared to which one will work the best. Obviously, the easiest thing to do would be to run it until the bolt shears off all the way. But, if you did that, you would be ignoring the grease fitting that needs to be replaced.
The first thing I would try would be to turn the bolt. Spray some kind of penetrating oil or lubricant on the bolt to help lubricate it if it turns. Spray this on from the threaded end of the bolt. Don’t be afraid to put some pressure on it. If it breaks off, that could be a good thing. It would get 1/3 of the bolt out.
If you get the bolt to rotate a couple of times, then you should be able to drive it out. as mentioned before, be careful not to mushroom the end of the bolt.
If it breaks off and part of the bolt comes out, put the nuts back on the other end and tighten them down. Keep tightening and see if you can break this end off too. If you manage to break the ends off but they are not deep enough, you can drill the bolt out down to the gear box shaft.
This should leave only the part in the middle. You should be able to get the shaft off then. There should be a lock ring on the end of the gearbox shaft to keep the PTO shaft from slipping off while it is running. Be sure to remove the lock ring. You may have to slide the shaft toward the gear box to remove this lock ring, then you can slide the shaft off.
The shaft may still be hard to slide if there are any burrs on the end of the broken bolt. You might be able to rotate it and slide it at the same time.
Hope this helps,
MIke