Are Civil War images in Harpers Weekly protected by copyright?

The long version: The original images are not protected by copyright, that has long expired. However, as with most legal questions, there are other factors to consider.

While the originals may be public domain if any editing or enhancements have been done to the photos (cropping, contrast/brightness adjustments, etc) the rights to those changes would, in all likelihood, belong to Harpers Weekly. Additionally the arrangement of the photos and any accompanying text, provided it qualifies as copyrightable, would also be protected.

The short version: No you probably can't "help yourself" to the photos & use them without permission.