Is it realistic to think that we can get out of bed in Varenna and be able to make it to the Milan airport for a noon-ish flight back to the US? Thanks for any help.
The 6:23 departure from Varenna-Esino station should allow you to connect at Milano Centrale and arrive to Malpensa by 9:00. There's also an earlier option. See www.trenitalia.com. Have tickets in hand in advance, whether you buy online, or in an earlier train station.
We always have spent the night at MXP with a morning flight. The train travel will make for a very long day added on to your international flight.
Another choice would be to stay in central Milan - it's great at night!