When you first talked to the guild master you should have had the option to ask about getting into the mine, at which point he should have given you the key. Apparently you didn't get that far, or the interruption reset something.
Who came upstairs, the original two that were on the first floor?
If so, maybe talking to the guild master before defeating them confused part of the game, or starting the conversation and then waiting so long before returning caused a problem.
What should happen is that after you get the key the guild master decides it is time to leave, and four black ring archers come upstairs (which I assumed were the 'they' you mentioned). You and the miners should be able to take them out on the stairs, and then there are 3 black ring warriors on the first floor.
Try emailing support@larian.com. With your save maybe they can reset the guild master, or give you the key.
