I had the same problem that Matt in the Evergreen State did with my doors. I inherited a house from my family here in The Tar Heel State and after my recent marriage, my wife and I decided to make it our home for a few years. It was a typical warbaby house, built in the 1940s and remodeled a time or two. It has a mix of plaster/paneling/drywall walls, a handful of fireplaces, and lots and lots of glass windows and doors. In fact, when I moved in all someone would have to do to take a stroll through the house was break a small pane on the door and reach through to turn the lock. Since then, I have been replacing locks with double-sided deadbolts and replacing doors. My front door was mostly glass pane with floor-to-ceiling windows on each side, like Matt's. I replaced the door, left the glass in the windows, and took half-inch plywood, cut to fit, and screwed a piece in on both the inside and outside of the glass. On the outside, I covered it with vinyl siding to match the exterior of the house, and on the inside I covered it with drywall so I could paint it to match the room color. Presto, not a piece of glass anywhere around the door someone could break through. I have left all of the windows untouched, but keep a stash of plywood handy in the barn so I could cover them quickly if need be.
Thanks for all you do. - A.