I have a similar situation in my family with my great-great-grandfather. While he died before his wife, I do not believe that wives had to be married at the time of the Civil War for them to receive the pension upon the soldier's death. My great-great grandfather was considering divorce from his second wife (after my great great grandmother died) and I have a letter from the Bureau of Pensions that said that his second wife would be entitled to half of his pension if they divorced. They were married in 1929. You can request information from the National Archives (they have a website but can't remember it) and obtain the FULL pension file ($100) and military record ($25). The two cost $100 but they do not charge your credit card if they cannot find the record.
Hope this helps...if you need more information, email me at chris_tracy76@yahoo.com
Chris Tracy