I have to agree with the other posters here. And for all the reasons they said and another one that sort of relates. If you use your marker with improvised ammo, it may malfunction, (I'm not a paintballer, but I think this is a general rule with projectile launchers.)
Also, using even functional improvised ammo may not be as effective as you think, a hardwood ball the size of a paintball would probably be heavier than a paint ball which would reduce velocity and energy.
The other thing is that even in a perfect situation regarding functionality, some people react very differently than you expect to pain in extreme situations. It may actually make the situation worse. They may become more determined to continue their assault. And if they win, and subdue you and your group, who do you think they are going to be pretty upset with? I've heard stories about how in vietnam, when a group of american soldiers were taken prisoner by the enemy, the guy with the shotgun didn't get taken prisoner. He got the shotgun used on him. The reason for this is that despite its fatal reputation, the shotgun is not always instantly fatal, it does a really good job of stopping the threat, but sometimes it takes a long painful time to die, and the vc hated shotguns for this reason. Thids may or may not be true, but the principle is sound, inflicting pain on people doesn't generally garner good will.
So, use the marker on pests, for fun, and trail marking. I would only use it for self defense, if it was in my hand or the only weapon near when I needed it. I would only use standard ammo and probably try to blast to the face if I could but I would givem as much of it as I could while trying to get as far away as possible as fast as possible, if possible.
Its not the worst idea I have heard, but its a pretty crappy way to plan when there are more effective measures to use.
If you were part of a group defending a property against a party of invaders or potential invaders, and you wanted a less lethal but still very effective method, look for some less lethal shotgun rounds, (I don't know if they are civilian avaiable) and things like tazers, and riot control pepper spray canisters, train, and carry and deploy those measures effectively. Just my thoughts on the matter. Just for balance, I have heard on news about invasions and crimes being stopped with paintball markers, but not often enough to plan it as a primary, secondary, or even tertiary or even quaternary measure. They were always instantaneous response scenarios and unplanned. Hope this helps you choose wisely one your tactics and equipment.