Foremost - the rude behavior by the hotel is an abomination, and whoever manages that property should be ashamed.

Second - if your wife's name was not on your reservation, why would you expect her to be able to check in? It seems like a basic security protocol to allow only guests whose names come up on the reservation. Of course at the point the hotel called you and you confirmed your wife should have access, the hotel should have apologized then and there for any inconvenience.

Third - I have never had a problem checking into Hilton and Hyatt hotels as a second guest, even when the method of payment is points or free night cert, and the primary guest never makes an appearance. I've always received the primary guest's elite benefits. I've never done this with SPG or Marriott hotels, however, and I've always called the hotel in advance to say I will be checking in first, without the primary guest present.