Several sources imply--but don't state outright--that the school still had a military component through 1860-61. It would certainly be odd for a school to still call itself a military school, but not have a cadet program.
Alexander left AMI to, among other things, start a military school at Pine Bluff, which was under the charge of J. J. Martin and L. W. Mears. Alexander appears to be living in Tulip in 1860, per the census--which would imply (but not prove) that the military component of AMI was still ongoing.
The relationship between AMI and St. John's College in Little Rock is what intrigues me. The founders of St. Johns were many of the same people (e.g., the Smiths) who were trustees at AMI. And SJ was founded as a military school. Did the AMI trustees in essence abandon the military component of AMI to restart the same program at Little Rock under the auspices of a new school? And if so, did St. Johns draw cadet arms from the arsenal?
What are your sources for the turning in of the arms to the arsenal?
I agree about the cannon. Thomas J. Key's diary says that Key's Helena Light artillery had a howitzer that once adorned the campus of AMI. Albaugh's book says the 2 cadet 6 pounders were captured 1-1-1864.