How can one atone for wrongfully taking money from the treasury when one is unable to return it after repentance?

All praise is due to Allah for your repentance, but your repentance is not complete until you return what is rightfully due to its owners or seek their forgiveness. Strive to return the stolen money, even if in installments, and you can borrow to repay the debt. If you are unable to return it, seek forgiveness from the shop owners and inform them of the debt. If they do not forgive you, then write them a document acknowledging the debt, so you can repay it when you are able. Doing this will absolve you, for Allah does not burden a soul beyond its capacity, and returning this right is more important than voluntary charity.