Personally, I think building a visitor's center that externally looks like the missing warehouse makes a lot of sense. The outward appearance would fit in with what the yard looked like when it was a working railroad. Yes, a warehouse like building would restrict the view from Terrace Avenue - just as it did when the D&RGW was running trains.
One of the issues we have to accept is how much the world has changed since 1968. People like having electric lights, indoor plumbing and paved streets, cell phones and the internet. We are not going to be able to eliminate cell phone towers, curbs and pavement, and the like from the towns on the remaining portions of the former D&RGW narrow gauge. One of the huge issues for a railroad like the C&TS is making itself more accessible and appealing to large numbers of visitors / riders who like living in 2007, and only want to visit the past. In a word - PARKING becomes a huge issue. Convenient parking - not a four to eight block walk from the railroad. Handicapped access is another. Yes, you are allowed some leeway in restoring National Register historic sites, but in many instances, you have to find a way to provide access.
These two issues are reasons why the rebuilt warehouse as visitors center seems logical to me. It is possible to have doors with ramps leading up to them, and easy access for people with mobility issues. Inside the building should have climate and humidity control, especially if it is to be part museum. If a basement is included, plan for an elevator to reach the basement. Parking is right outside, and not too far from the depot.
Now, beyond that, additional parking is going to be an issue - and it would be wise to start planning NOW for where it can go, and how to pay for obtaining land needed for additional parking, and remaining on good terms with the rest of the Chama community. Because if the railroad becomes as successful as we all want it to be, there will need to be room for more autos to park.