We are hoping to use the Swiss Card to fully cover the last day of my trip leaving from Murren to Zurich to fly out. The rule of "one trip out by the fastest, most direct route" unsettles me. On the map, it looks direct to me: Murren-Interlaken-Lucern-Zurich, but how can I be sure the train officials will agree? Also, we would like to have a layover in Lucern for several hours of sightseeing. Will that disqualify it as "one" trip?
Just ask the person at any rail ticket counter. I really like the little rail station in Mürren because it's not a bustling place and the workers are very nice.
You will be fine. That is actually the "most direct" route, although not the "fastest"---that one goes through Bern and costs more. And yes, you can stop for several hours in Luzern on your way.
There are two banks of lockers at track level where you can store you rbags while sightseeing.
The "direct route" rule is just to keep you from zigzagging all over the place on that trip.
I haven't used a Swiss Card for several years, so I don't remember if there is a little box on the pass for you to enter your last date of travel. If there is, be sure and write in the date before you start the trip on that day.