Clearly the church accepted the donations in good faith. That said, it was stolen property. Generally stolen property is subject to legal clawback as long as the crime is not outside the applicable statute of limitations. (In those cases the law gets murky and there is some variation between jurisdictions.) Unfortunately the law does not offer much relief for whoever has the misfortune of holding the hot goods at the time it is discovered that they belong to someone else. The only exception would be if they church actually did not have the money or it would be bankrupted by its return. In such a case they might be able to argue in court that it was simply not in their power to return it. However, I don’t think that this is the case.
In any event, and legal questions aside, morally the church has no claim to the money and it must be returned. A victim of theft does not lose claim to their property because it has been fenced or passed on by the thief.
What you said. Excellent description of the issue at hand.