What is the ruling on obtaining an Istisna' (manufacturing) agricultural loan where the amount is paid back over years with a slight increase over the principal, knowing that the lending party agreed to purchase the commodity and then disbursed a sum of money to the beneficiary?

The transaction mentioned in the question is an interest-bearing loan (riba-based loan). Therefore, it is impermissible to borrow with an increase, because the interest on a loan is forbidden by scholarly consensus, whether it is much or little. Every loan that draws a benefit is usury (riba).