Three nights in the Swiss Alps (Milan - Zurich)

Two nights is one full day. Half of your other days will be spent on transit. Don't under-estimate how long transitioning between places actually takes. If there's any way to spend more time in Wengen /Murren, do it. No one is ever ready to leave.
Download the SBB app for Swiss trains.
Sorry, I'm not sure it's worth going to Switzerland for two nights, and flying out of Zurich.

IF you had the time-
Milan to Tirano, Italy
Tirano , Italy to catch the Bernina Express to Pontressina,
Pontressina to the Berner Oberland,
BO to Zurich.

I love all things Swiss, but I don't know how to keep you from spending all your time riding trains.
Have a great adventure!

I think the key here is, what time is your flight departing Zurich? If you only have 2 nights, one or those may have to be Zurich for your flight the next day. If that is the case, you only have time for 1 night in Pontresina like this.
Day 1. Train from Milano Centrale to Tirano, then change to a train to Pontresina. Night in Pontressina.
Day 2. Train from Pontresina to Chur, then train to a train to Zurich. Night in Zurich.
Day 3. Train to Zurich airport. flight home.

That will give you an afternoon and evening in Pontresina, followed by a morning and afternoon in Pontresina.

Thanks for the replies and information. We're actually really excited about the train rides, just because it's something we never get to experience in 'real life' here at home. All said, I know it's lot of travel, but we're viewing it as part of the experience and looking forward to the site seeing from our seats :)

Another possibility for spending a night along the Bernina rail route might be Alp Grum which is a few stops before Pontresina coming from Tirano. There was a thread here a few monts ago with a link to an article about a hotel there. Pontresina would also be a nice place to stay.

I apologize, it's actually 3 nights in Switzerland with the last being spent near the airport in Zurich. I've edited the original post