While I cannot comment on the efficacious of blasting it, as to the question of damaging the track (further) the answer is likely "yes". If you are using a mechanical means to scrub the rust away, you almost assuredly will also blast away what remains of the plating that is (or, rather, should be) keeping it from rusting in the first place. That being said...if the track is already very rusted you probably don't have much to lose. Wiping down the blasted track with a light coat of oil may help retard the rust returning once it's clean, but you will likely have to rinse-and-repeat the procedure at some point not too far down the line.
Before blasting, though, a question: do you have rust on the rails or is it just discolored and grimy/dirty? If the latter, there's probably no need to resort to blasting but rather you should focus on just cleaning first. You might be surprised at how well it works once cleaned with rubbing alcohol, naptha, etc.