Very interesting. Two points to mention. The first involves colleges having a Baptist affiliation before the war; and second, Baptist chaplains assigned to units during the war:
Colleges/Seminaries with Baptist affiliations:
-Allegheny College, Blue Sulphur Springs, (West) Virginia (opened 1859, closed 1861, burned by the Federals in 1864).
-Central University of Iowa, Pella, Iowa.
-Furman University, Greenville, South Carolina (founded 1826).
-Denison University, Granville, Ohio (founded 1831), known as Granville College 1845-1852.
-Howard College, Marion, Alabama (founded 1841), now Samford University.
-Mercer University, Penfield, Georgia (first class in 1841).
-Mississippi College, Clinton, Mississippi (founded 1826), with a Presbyterian and Baptist affiliation.
-New York Central College, McGraw, New York (founded 1849, closed 1860).
-Southern Baptist Theological Seminary, Greenville, South Carolina.
-Southwestern Baptist University, Murfreesboro, Tennessee (afterwards Union University, Jackson, Tennessee).
-Union University, Murfreesboro, Tennessee (founded 1851, closed April 1861).
-University of Rochester, Rochester, New York (founded 1850).
-Waterville College, Waterville, Maine (established 1813), now Colby College.
Identified Baptist chaplains who served at Gettysburg, all except the last with the Confederate army:
-J. A. Stradley (identified as a missionary), 2nd North Carolina
-Crawford H. Toy, 53rd Georgia (co-founded Freemason Street Baptist Church in Norfolk, Virginia).
-John L. Pettigrew, 31st Georgia.
-Henry E. Brooks, 2nd North Carolina Battalion.
-W. B. Carson, 14th South Carolina.
-Augustus Goodwin Raines, 14th Alabama.
-Asa Monroe Marshall, Sr., 12th Georgia.
-Henry Carrier Vogel (or Vogell), 61st New York (possibly present), studied at Baptist Theological Seminary.