If the crew's presence caused damage then they should have to pay for it. It appears that as of July 2016, the house was sold to an unnamed buyer. It does seem that the house drew a lot of tourists, and that would have been because of the film, but not because the crew did anything to damage the property.
If a movie filming in a location somehow causes property values to decline, the producers should be held financially responsible. The area was a part of the movie. If the same movie crew caused physical damage to property while filming, they would be held accountable. The same should hold true if they have a negative economic impact on an area.
Buffalo Bill's house is not unsellable soley because of the movie. People may be afraid of this (fictional) villian, but it is suprising that a fan of the movie would not want to buy it. There are a great deal of factors involved in selling a house, and it is hardly fair to blame a movie crew.
While I do not believe filmmakers should pay for depreciation costs, perhaps an upfront cost agreement beforehand might be useful. As Buffalo Bill's house is a primary example, the contract should have included a nominal fee for the unknown depreciation that may or may not occur. Filmmakers cannot predict the future, so they should not be responsible for what happens in the future.