Is it obligatory to return money taken from the the father's workplace to the original owner of the shop, or is this money considered a rightful entitlement for the questioner by way of common good?

You erred by taking the shop owner's money, even though your father was the one who asked you to help in exchange for money. You must perform sincere repentance for the theft and return the money you took to its owner by any means you deem appropriate.