That is a real quandary, because we need more trains in this world and fewer cars, but the Yucatan, as we now know with Lidar studies, was pretty densely populated. It's sort of a case of no matter where you put it, you're going to damage possibly essential archaeology and there isn't a reasonable enough amount of time to excavate it all before putting a rail line through.
That said, from the sound of things, they're just moving forward at breakneck speed and filling cenotes instead of building bridges, so this could be done with a lot less damage.