How can the University tell me what I can't do with these photos if they were taken by government entities during the Civil War?
Don't confuse "ownership" with "copyright holder" - the two can be separate legal entities. For example, if I'm commissioned to take photos for a magazine then I own the copyright to the photos but the magazine owns the photos themselves. This means (1) they can't use the photos without my permission since I own the copyright but also (2) I can't use the photos without the magazine's permission since they own the photos themselves.
If the photos are out of copyright that does not mean they are in the public domain - it simply means the original artist no longer has a claim to them. But it is still up to the owner to decide what can and can't be done with them. They might have paid tens of thousands of dollars for the photos so why should you get to copy them for free? ;)
Most copyright matters can be resolved amicably but you really should have contacted the University up-front before using the pictures - they might have been more agreeable to what you were doing if you explained your site beforehand.