It's unfortunate that an Amtrak employee would not let you stand on the platform. Did you explain that you were watching your wife depart?
I assume that Amtrak doesn't have an official policy of prohibiting people accompanying a passenger from witnessing a departure at most stations. I believe non ticketed passengers are not allowed on platforms at some big city stations like New York and Philadelphia and Portland.
Unfortunately what seems like an innocent action of watching the train leave could be interpreted by an overzealous employee as a security threat. People planning terrorist attacks at train stations and other places have been known to check out a potential target by observing the area beforehand so now days everyone is a suspect.
You should email Amtrak customer service with specifics about the date and time and description of the employee and details about the problems in the room.
I'm pretty sure Amtrak will refund some of the cost of the room or offer a voucher for a future trip.