Does my work in programming a system used in usurious transactions count as aiding in usury, and what should I do with the money I earned from this work?

If the bank's role in the transaction is limited to financing with interest, then this is an usurious transaction. However, if the bank genuinely purchases the commodity and then sells it in installments at a higher price than the immediate cash price, there is no harm, provided that the price is not increased if the client delays payment.

If you know that the transaction is forbidden, then your work is forbidden and your wages are forbidden. You must repent and dispose of any remaining wages by spending them on charitable causes.

However, if you were ignorant of the prohibition, then there is no sin upon you, and you may benefit from the wages that were determined for you.

It is stated in the fatwas of the Permanent Committee and Ibn Uthaymeen that whoever earns unlawful money while knowing of its prohibition must dispose of it by spending it on righteous deeds. But if they were unaware of the prohibition, then what they earned is theirs.