True, the Interstate Compact states that the purpose of the railroad is "to promote the public welfare by encouraging and facilitating recreation and by preserving, as a living museum for future generations, a mode of transportation that helped in the development and promotion of the territories and states"
"promote the public welfare by encouraging and facilitating recreation" is just as important as "preserving, as a living museum for future generations". Promoting the public welfare includes economic development.
Without the C&TS Chama would much smaller, and might even be a ghost town. Antonito would be around but would be a bit smaller as well.
For New Mexico, the railroad is a very important economic driver for the Chama area, and that has been given as the reason many times by the New Mexico legislature to continue funding the railroad.
If it comes down to being forced to convert the coal fired locomotives to oil fired, I would much rather see that happen that having the railroad not be allowed to operate, and turning into a static display type museum.
Any operating railroad, museum or not has to be make adjustments due to economic and political pressures. If you cannot adapt, you cannot continue to exist.