Best way to avoid (as much as can be) the zoo at Gettysburg is to use the tape-recorded self tour, especially if you've done a little homework ahead of time. The battlefield itself is spread over quite a large area and most of the crowds cluster around the visitors' centers.
If you get a chance to go up the Shenandoah Valley, I highly recommend the battlefield at New Market. The battlefield itself is pretty well preserved (excepting the interstate running right through it) and the museum is excellent. Usually very uncrowded, too.
The Appomatox site has a lot of interesting historical information, but there wasn't a setpiece battle fought there, so it's mostly recreations, but still worth a visit.
I haven't been to Antietam yet, myself.
As far as non-belligerent activities go, you might want to check out the websites of the Virginia tourism people. Virginia has attractions for an incredible range of interests. One of the standard places to visit is the Luray Caverns near New Market.
I hope you have a good visit. Cheers
-HM