Dowtown Middlebury is currently the scene of lots of construction (as you will have seen when you visited), based around the need to replace two 1920s bridges over the railroad (see https://vtrans.vermont.gov/projects/middlebury).
Once construction wraps up in the summer of 2021, Amtrak will/should/is supposed to begin service from NY Penn to Burlington by extending the existing daily “Ethan Allen” train from Rutland to Burlington. This will see one train each way/day, probably leaving NY early/mid-afternoon, and arriving in Midd about 9pm. The return service will leave Burlington first thing in the morning, getting to NY Penn in early afternoon.
If your daughter is applying to start at Midd in Sep 2020, she’ll have the train for two or three of her four years - it’ll be a great boon for the students and the College.