We were planning on taking the Glacier Express from Chur (staying in Pontresina) to Zermatt but the Glacier is sold out for our dates in September. Only other options is to travel back to Zurich then to Bern and to Zermatt. Any other options or other trains travel on the same rail as the Glacier?
Yes, just check the schedule at www.sbb.ch/en and put in Chur to Zermatt via Disentis/Muster. You will see lots of trains, but you will have to change trains at Disentis/Muster, Andermatt, and Visp (or Brig).
PS You just saved the 49 CHF seat reservation fee.
https://community.ricksteves.com/travel-forum/switzerland/regional-trains-in-switzerland
Just ride the regional trains that use the same tracks. See the above Search link. Safe travels!