I've stayed in the Hilton Tallinn, and frankly, it's a wonderful hotel. I also paid 12k points and €38, booked before the recent program changes.
Whether the night auditor actually made the change, it has nothing to do with the shadiness of the hotel. I suspect it wasn't the night auditor, but rather a system bug related to the program changes that has been reported on here, though I can't easily find a reference. It may even be that the night auditor tried to upgrade the room for you in advance (I had a very nice suite upgrade) and that triggered the charge.
I have stayed in several eastern European Hilton properties and virtually all of them have been very good indeed - both compared to those in western Europe and the US, and the local standards for their market. I certainly wouldn't besmirch half a continent over a system bug that didn't start there.