The Dunker Church survived the battle and was repaired and reused for some time thereafter. Eventually the congregation moved and the building fell into disrepair, helped along by souvenir hunters. It collapsed in 1921. A house was later built on the original foundation. This became a gas station and eventually a souvenir shop. The site was finally purchased by a private conservancy group and donated to the NPS. The church that you see today is a reconstruction done for the centennial in 1962. There was plenty of documentary evidence for the original structure so the reconstruction is quite exact.
P.S. Like most of the other Civil War battlefield parks, Antietam started as a ribbon park, with most of the land still privately owned and the Park Service owning a few key spots for interpretation. Many battlefields, including Fredericksburg, Chancellorsville and the Wilderness in this area, began this way, and were then overrun by modern development. Even at Gettysburg, the first day's field is severely compromised. Antietam is one of the best examples of park where early and persistent conservation outran the developers. Most of the acreage at Antietam was actually acquired by private heritage groups and donated to the NPS. It was only about four years ago that the Civil War Trust (now the American Battlefield Trust) acquired the D.R. Miller farmhouse, barn and immediately surrounding acreage. (This is the triangular piece of land immediately south of the Cornfield, bordered by the Hagerstown Pike, Cornfield Road and the Smoketown Road.) Most people have probably assumed that this area was long a part of the park. Not so. The Mumma and Roulette farms are also recent acquisitions. (This is the area immediately in front of Bloody Lane, across which the federal attacked. There have been other recent acquisitions as well, but these two tracts are as important as core battlefield can be; they rank with The Angle and Little Round Top at Gettysburg. And now you can walk the ground. If you've not been to Antietam within the last five years, go again. You will see major changes, all for the good. The park is still growing.
Second Manassas is also being pieced back together, and Perryville is darn near complete, with a big piece of the puzzle on the center of the Union line just being acquired last year. Most of the current preservation is being done by private organizations. There are Friends groups for many of the larger battlefields and quite a network of local and regional groups. The American Battlefield Trust (battlefields.org) is the big national group. If you are looking for a giving venue this Christmas season, check it out.