Here is an option which you could consider. Two days makes it kind of tight (if I have your timing correct- I'm a little uncertain about what you do after Chur. But it is not impossible, and has slack time to look around a bit built in. It includes the Matterhorn.
Checking your available time:
<<"We will conclude our river cruise on Oct. 17. Had hoped to take train from Zurich to Zermatt that day and then Glacier Express from Zermatt to Chur on the 18th.">>
<<"We only have 2 days due to a deadline for our return home,">>
That implies that you will return to your departure airport (presumably Zürich) on the night of the 18th? Is that correct?
An Alternative including the Jungfrau Region -
For guidance on the overall geography, I suggest this map:
Since the mountains determine the location of the train routes, it is helpful to zoom in to the point where the train lines show up:
Follow your original plan to got to Zermatt on arrival. Look at the Matterhorn, possibly from Gornergrat, if there is no cloud cover to interfere.
Many river cruises end at Basel; I was not aware that they end at Zürich, but it is certainly possible. Basel to Zermatt takes 3 hours 15 minutes. Zürich to Zermatt takes 3 hours and 12 or 19 minutes.
Second day -
Total trip -
Zermatt to Wengen, then Wengen to Zürich airport. Each section approximately 3 hours.
First part - Zermatt to Wengen, via Interlaken Ost and Lauterbrunnen
Depart 0813, arrive Wengen 1119. Uses the newest piece of rail technology on that choice of routes.... a boring but fast tunnel underneath the Alps from Visp to near Spiez, then onward to Interlaken Ost.
Other service every half hour, more or less, at xx13 and xx37. That assumes that no snowfalls like the current one block travel. ;-)
Cograil from IO to Lauterbrunnen - very scenic cograil from Lauterbrunnen to Wengen. As you pull into Wengen, you get a quick glimpse along the Valley, essentially what is shown in the attached image.
Wengen is a nice village Nice scenery , and plenty of restaurants and shops. Walk north 10-15 minutes from the train station to the viewpoint by the church to see that view along the valley...weather permitting. Have lunch at the Hotel Bellevue if you want to see that scenery while you eat.
Check this link for a map..scroll down:
Depending on how much time you want to spend looking around or exploring further, eventually take the train back down to Lauterbrunnen, then IO, and onward to Zürich or the airport. Many trains per hour from Zürich to the airport, which take 9 to 20 minutes. I used Zürich as a destination, because I was not sure what your timing is.
Wengen to Zürich
Depart 1603, arrive Zürich in 2 hrs 55 minutes at 1858. Every 30 minutes at xx03 and xx33.
Options at Wengen -
During the 5 hours I have proposed at Wengen, you could as an option, ride the very scenic cograil from Wengen to Kleine Scheidegg, possibly even to the Jungfraujoch.
To the Jungfraujoch, change at Kleine Scheidegg, 1 hr 11 minutes at xx24 and xx54 all day. Hangout for a while, return at xx13 and xx43, one hour 16 minutes to Wengen, and approx. 3 hours more to Zürich.
However, if I were doing it, not being enamored of the quite expensive trip to Jungfraujoch. I'd possibly ride as far as Kleine Scheidegg, get out , look around, and return to Zurich via Grindelwld and IO.
All the sightseeing depends on having clear weather. Good chance in October,but not guaranteed.
Leave your luggage at IO - lockers and left luggage office)
(Check the map that I linked earlier to understand that.)
Actually, my own preference after arriving in Wengen would be to walk 5-8 minutes to the cableway to Männlichen, up above Wengen. Ride up. 5 minute ride, every 20 minutes.
Have lunch there. Look around, walk a bit, return. There is grand and stunningly scenic easy walk from Männlichen to Kleine Scheidegg, but the timing might be tight , unless your prepared to walk quickly. Nominal 1 hour and 1/2, but it takes me a good deal longer because I look around a lot and take photographs.
Nicknamed "The Grannies' Walk. I'd not suggest it unless you had absolutely stunning clear sunny weather, and could take a later arrival to Zürich than 1858 if you get slowed down. People do it in sneakers ( training shoes) but you need good grippy soles for the gravel path on downhill sections. I wear boots to help my ankles, but they are not critical.
Sounds complex. Is not really, and there is plenty of backup contingency transport typically a half hour later (cableways only until late afternoon) if you miss a train.
Pictures around Wengen and Männlichen attached. Männlichen Gipfel is a little peak about 100 meters higher, overlooking the top station of the cableway at Männlichen.. Picture attached.
Switzerland offers far too many wonderful options. The Glacier Express is a terrific, easy journey. But, it is also easy to use the wonderful transport system, so , it is easy to explore the other options.