As far as I understand it, and I am happy to be proven wrong, there is no legal right that farmers have to defend themselves with any form of air gun etc. This might be something they use to try and scare them off but should they shoot and injury a trespasser for example by shooting them in the eye. The farmer could land in some pretty hot water. Terms like "reasonable force" would come up and shooting someone in the eye for trespassing would probably not fall into that category.
I believe the rules are like this to stop vigilantes laying down the law. As it is a fine line from, I was protecting my family so had to shoot the burglar and it is his/her own fault if they are injured or die. To the next step of needing to keep a marker, knive, gun, etc on you to protect yourself/family when your out.
Even though air rifles, markers etc are not weapons designed to kill humans they can still inflict very serious amounts of damage. A friend at school was shot in the stomach by an air rifle at close range (do not know if it was FAC grade or not) and he was in hospital for quite a while. I was involved in an unfortunate incident where I was shot in the eye in a safe zone at a tourny a couple of years back with a paintball and almost lost that eye.
I understand your opinion but if this happened then the yobs outside would just have markers, airguns etc too and start wearing masks anyway. Then you are in a worse position as they can cause even more damage.
I am glad it is this way as opposed to the very "liberal" use of guns in the US. Which has caused high gun crime rates, etc.
If you want to protect yourself make your home as secure as you can and if things get out of hand call the police. Let them do their jobs. For when you go out maybe take a self defense course and learn about some of the techniques to minimise trouble in the first place and how to deal with things should they get out of control.