Leaded glass windows are not bulletproof glass, it's just glass in a gridwork of lead. If you threw a rock at it, it would still break. Go chuck some rocks at stained glass windows at a church downtown and see how they feel about it. (Don't do this.)
If windows could actually be broken the fix would be shutters, but that would be a pain because windows can't be opened to close the shutters from inside (which would also let drifters in). No one wants to have to run laps around the house closing all the shutters outside before dark.
Also I do not have a castle. I have a few one- to two-story cobblestone houses. One has a fenced in front yard, but building a moat never occurred to me.
Slap a window up, go outside, put a solid block over it, then chisel away in the desired pattern. Unless I'm mistaken, projectiles would hit the chiseled block even if 90% of it is gone.