Pardon the long article, but I lost several sources from yesterday's research so wanted to put the rest down before I lost them too! Lots and lots of searching for this one!
The professor of chemistry at VMI from 1846 to 1861 was William Gilham. After the war he became president of Southern Fertilizer Co. in Richmond and died in 1872. After hours of searching, I found two assistant professors of chemistry at VMI before the Civil War. Both were listed as under Gilham, not Jackson.
One was Robert E. Rodes, who left when Jackson arrived, because he wanted the same position (wikipedia, "Robert E. Rodes"). Since Rodes was killed at 3rd Winchester, he's definitely not our man. As of 1855, he's the only assistant professor of chemistry listed. The other was Mark Bernard Hardin per https://books.google.com/books?id=CjwUAAAAYAAJ&pg=RA4-PA27&lpg=RA4-PA27&dq=assistant+professor+of+chemistry+vmi+under+Thomas+Jackson&source=bl&ots=BhFb-leMit&sig=erqx0ROf58VBT9ZCKj5iu5r-mVo&hl=en&sa=X&ved=0ahUKEwjE9oPm_-_SAhUTzGMKHUvZBbQQ6AEIQzAG#v=onepage&q=assistant professor of chemistry vmi under Thomas Jackson&f=false. He was there from 1858-61 per
http://ead.lib.virginia.edu/vivaxtf/view?docId=vmi/vilxv00068.xml. A
http://socialarchive.iath.virginia.edu/ark:/99166/w6322jnb
https://www.clemsonwiki.com/wiki/Mark_Bernard_Hardin
In none of these sources can I find that he served on any US commission after the war.
Just as a wild guess (mentioned in one of the sources I lost when searching for US commissions post-CW), I tried the US Commision of Fisheries. Eureka, I have found it! Our guy is
Marshall McDonald. Per the wikipedia article of the same name, the details match. He taught at VMI both just before (860-61) and after the war. During the war he was an engineer under (among others) Jackson, Pemberton, and Bragg, reaching the rank of brigadier general. In 1875 he became interested in fish farming, developed a fish ladder, and was Fish Commissioner of Virginia. In 1879 he was appointed to the
United States Commision on Fish and Fisheries. He was named Commissioner of Fish and Fisheries in 1888.