The only real defense against it is either an absurd amount of defenses in a corner or you have a player standing guard there. And that is flat out ridiculous. It is like saying "If you don't want your house to burn down, station a fireman inside it". They removed the water in the middle towers because that was gamebreaking but upgraded walls? Did really need to put a handicap access ramp and door to the bank vault for the ethically challenged?
Actually they removed the water from the middle of the map for one main reason - to stop fly-hacking. Apparently it basically surrounds you in water, making the game think your swimming and hence you can fly through mid air. They removed the water and added code that detects swimming, so any character that enters a 'swimming' state within siege just gets insta killed or 'Sniper Bunnied'.
This is also why those that claim a guild fly-hacked over their walls to take down procs etc is now false, the only way to get in is by jumping over the back of the castle wall or using r/wd and glitching gates sideways.